Changeset 4512


Ignore:
Timestamp:
Aug 15, 2013, 5:14:34 PM (10 years ago)
Author:
Fredrik Levander
Message:

Fixes #809. Fixed reporting of static modifications when no variable modifications present.

Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • trunk/api/core/src/org/proteios/core/ObservedModification.java

    r4502 r4512  
    156156      List<SearchModification> fixedMods, ItemFactory factory)
    157157  {
    158     if (description == null || !description.contains(" "))
     158    if (description == null)
    159159      return new ArrayList<ObservedModification>();
     160    if (!description.contains(" "))
     161    {
     162      return getModList(description, null, fixedMods, factory);
     163    }
    160164    String[] s = description.split(" ", 2);
    161165    return getModList(s[0], s[1], fixedMods, factory);

  • trunk/plugin/src/org/proteios/plugins/PrideExportPlugin.java

    r4510 r4512  
    24022402
    24032403
    2404   /**
    2405    * Writes PRIDE XML cvParam(s)/userParam(s) for reporting a potential
    2406    * peptide modification. The modification information is taken from the part
    2407    * of the peptide description after the first space. The modification
    2408    * information is interpreted according to what search engine was used. The
    2409    * search engine is inferred from the score type in the hits query. If data
    2410    * could not be obtained to create a PRIDE XML cvParam for peptide
    2411    * modification, null is returned.
    2412    *
    2413    * @param dc DbControl The DbControl to use.
    2414    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    2415    *        XMLCrudeWriterImpl to use.
    2416    * @param currentHit Hit The hit instance to get info from.
    2417    */
    2418   private void writePeptideModificationInfo(DbControl dc,
    2419       XMLCrudeWriter xmlCrudeWriterImpl, Hit currentHit)
    2420   {
    2421     // Skip if not peptide
    2422     Boolean isProtein = currentHit.isProtein();
    2423     log.debug("isProtein from hit query = " + isProtein);
    2424     if (isProtein == null)
    2425     {
    2426       // Default is protein
    2427       isProtein = true;
    2428     }
    2429     log.debug("isProtein = " + isProtein);
    2430     if (isProtein)
    2431     {
    2432       return;
    2433     }
    2434     //
    2435     // Get information from spectrum search
    2436     // writePeptideModificationInfoFromSpectrumSearch(dc,
    2437     // xmlCrudeWriterImpl,
    2438     // currentHit);
    2439     //
    2440     // Get information from hit description
    2441     // writePeptideModificationInfoFromHitDescription(xmlCrudeWriterImpl,
    2442     // currentHit);
    2443   }
     2404
    24442405
    24452406
    … …  
    24642425
    24652426
    2466   /**
    2467    * Writes PRIDE XML cvParam(s)/userParam(s) for a potential peptide
    2468    * modification. The modification information is taken from a database
    2469    * SpectrumSearch query for the hit in question.
    2470    *
    2471    * @param dc DbControl The DbControl to use.
    2472    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    2473    *        XMLCrudeWriterImpl to use.
    2474    * @param currentHit Hit The hit instance to get info from.
    2475    */
    2476   private void writePeptideModificationInfoFromSpectrumSearch(DbControl dc,
    2477       XMLCrudeWriter xmlCrudeWriterImpl, Hit currentHit)
    2478   {
    2479     // Skip if not peptide
    2480     Boolean isProtein = currentHit.isProtein();
    2481     log.debug("isProtein from hit query = " + isProtein);
    2482     if (isProtein == null)
    2483     {
    2484       // Default is protein
    2485       isProtein = true;
    2486     }
    2487     log.debug("isProtein = " + isProtein);
    2488     if (isProtein)
    2489     {
    2490       return;
    2491     }
    2492     //
    2493     // Get information from spectrum search
    2494     File searchFile = currentHit.getIdentificationResultFile();
    2495     ItemQuery<SpectrumSearch> ssQuery = SpectrumSearch.getQuery();
    2496     ssQuery.restrict(Restrictions.eq(Hql.property("resultFile"),
    2497       Hql.entity(searchFile)));
    2498     ItemResultIterator<SpectrumSearch> ssit = ssQuery.iterate(dc);
    2499     int spectrumSearchHits = 0;
    2500     while (ssit.hasNext())
    2501     {
    2502       SpectrumSearch ss = ssit.next();
    2503       spectrumSearchHits++;
    2504       log.debug("ss.getAnalysisTime() = " + ss.getAnalysisTime() + ", currentHit.getRetentionTimeInMinutes() = " + currentHit
    2505         .getRetentionTimeInMinutes());
    2506       //
    2507       Iterator<SearchModification> smit = ss.getSearchModifications()
    2508         .iterator();
    2509       int searchModificationHits = 0;
    2510       while (smit.hasNext())
    2511       {
    2512         SearchModification smod = smit.next();
    2513         searchModificationHits++;
    2514         boolean isVariable = false;
    2515         float averageMass = smod.getAverageMass();
    2516         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": averageMass = " + averageMass + " currentHit.getExperimentalMassInDaltons() = " + currentHit
    2517           .getExperimentalMassInDaltons() + " currentHit.getMwInDaltons() = " + currentHit
    2518           .getMwInDaltons());
    2519         String modName = smod.getName();
    2520         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": modName = \"" + modName + "\"");
    2521         String modDescription = smod.getDescription();
    2522         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": modDescription = \"" + modDescription + "\"");
    2523         String cVid = smod.getCvId();
    2524         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": cVid = \"" + cVid + "\"");
    2525         boolean isFixed = smod.isFixed();
    2526         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": isFixed = " + isFixed);
    2527         boolean isSubstitutionModification = smod
    2528           .isSubstitutionModification();
    2529         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": isSubstitutionModification = " + isSubstitutionModification);
    2530         SearchModification.TerminalSpecificity terminalSpecificity = smod
    2531           .getTerminalSpecificity();
    2532         String terminalSpecificityStr = "" + terminalSpecificity;
    2533         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": terminalSpecificity = " + terminalSpecificity);
    2534         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": terminalSpecificityStr = " + terminalSpecificityStr);
    2535         int position = smod.getPosition();
    2536         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": position = " + position);
    2537         String aminoAcidSpecificity = smod.getAminoAcidSpecificity();
    2538         log.debug("SpectrumSearchHit " + spectrumSearchHits + ", SearchModificationHit " + searchModificationHits + ": aminoAcidSpecificity = \"" + aminoAcidSpecificity + "\"");
    2539         //
    2540         String idStr;
    2541         String nameStr;
    2542         String valueStr;
    2543         //
    2544         // Report modification as PRIDE cvParam
    2545         idStr = new String("");
    2546         nameStr = new String("");
    2547         valueStr = new String("");
    2548         // Construct modification PRIDE cvParam name component
    2549         if (isFixed)
    2550         {
    2551           idStr = new String("PRIDE:0000072");
    2552           nameStr = new String("Fixed modification setting");
    2553         }
    2554         else if (isSubstitutionModification)
    2555         {
    2556           idStr = new String("");
    2557           nameStr = new String("");
    2558         }
    2559         else
    2560         {
    2561           isVariable = true;
    2562           idStr = new String("PRIDE:0000073");
    2563           nameStr = new String("Variable modification setting");
    2564         }
    2565         // Construct modification PRIDE cvParam value component
    2566         if (modName != null)
    2567         {
    2568           valueStr = new String(modName);
    2569         }
    2570         //
    2571         // Write modification PRIDE cvParam if name property is set
    2572         if (nameStr != null && !nameStr.equals(""))
    2573         {
    2574           // Write modification PRIDE cvParam for fixed modification
    2575           // if peptide contains affected amino acid
    2576           if (isFixed && aminoAcidSpecificity != null && !aminoAcidSpecificity
    2577             .equals(""))
    2578           {
    2579             String peptideSequence = fetchPeptideSequenceFromHitDescription(currentHit);
    2580             log.debug("peptideSequence = " + peptideSequence);
    2581             if (peptideSequence != null && !peptideSequence
    2582               .equals(""))
    2583             {
    2584               if (peptideSequence.contains(aminoAcidSpecificity))
    2585               {
    2586                 String cvParamStr = new String(
    2587                   "cvParam cvLabel=\"PRIDE\" accession=\"" + idStr + "\" name=\"" + nameStr + "\" value=\"" + valueStr + "\" ");
    2588                 log.debug("peakListFile = " + peakListFile + " cvParamStr = \"" + cvParamStr + "\"");
    2589                 // Write modification cvParam
    2590                 writeCvParam(xmlCrudeWriterImpl, cvParamStr);
    2591               }
    2592             }
    2593           }
    2594           // Write modification PRIDE cvParam for variable
    2595           // modification if peptide description supports it
    2596           List<String> peptideModTargetList = fetchPeptideModificationTargetListFromHitDescription(currentHit);
    2597           log.debug("peptideModTargetList = " + peptideModTargetList);
    2598           if (isVariable && peptideModTargetList != null && peptideModTargetList
    2599             .size() > 0)
    2600           {
    2601             String peptideModTarget = peptideModTargetList.get(0);
    2602             log.debug("peptideModTarget = " + peptideModTarget);
    2603             if (peptideModTarget != null && !peptideModTarget
    2604               .equals(""))
    2605             {
    2606               String cvParamStr = new String(
    2607                 "cvParam cvLabel=\"PRIDE\" accession=\"" + idStr + "\" name=\"" + nameStr + "\" value=\"" + valueStr + "\" ");
    2608               log.debug("peakListFile = " + peakListFile + " cvParamStr = \"" + cvParamStr + "\"");
    2609               // Write modification cvParam
    2610               writeCvParam(xmlCrudeWriterImpl, cvParamStr);
    2611             }
    2612           }
    2613         }
    2614         //
    2615         // Report modification as PRIDE userParam
    2616         nameStr = new String("");
    2617         valueStr = new String("");
    2618         // Construct modification PRIDE userParam name component
    2619         if (isFixed)
    2620         {
    2621           nameStr = new String("Fixed modification setting");
    2622         }
    2623         else if (isSubstitutionModification)
    2624         {
    2625           nameStr = new String("Substitution modification setting");
    2626         }
    2627         else
    2628         {
    2629           nameStr = new String("Variable modification setting");
    2630         }
    2631         // Construct modification PRIDE userParam value component
    2632         if (modName != null)
    2633         {
    2634           valueStr = addComponentString(valueStr,
    2635             "Name = '" + modName + "'");
    2636         }
    2637         if (modDescription != null)
    2638         {
    2639           valueStr = addComponentString(valueStr,
    2640             "Description = '" + modDescription + "'");
    2641         }
    2642         if (terminalSpecificityStr != null)
    2643         {
    2644           valueStr = addComponentString(valueStr,
    2645             "Terminal specificity = " + terminalSpecificityStr);
    2646         }
    2647         if (position > 0)
    2648         {
    2649           valueStr = addComponentString(valueStr,
    2650             "Position = " + position);
    2651         }
    2652         if (aminoAcidSpecificity != null)
    2653         {
    2654           valueStr = addComponentString(valueStr,
    2655             "Amino acid specificity = " + aminoAcidSpecificity);
    2656         }
    2657         if (cVid != null)
    2658         {
    2659           valueStr = addComponentString(valueStr,
    2660             "cVid = '" + cVid + "'");
    2661         }
    2662         // Write modification PRIDE userParam if name property is set
    2663         if (nameStr != null && !nameStr.equals(""))
    2664         {
    2665           // Write modification PRIDE userParam for fixed modification
    2666           // if peptide contains affected amino acid
    2667           if (isFixed && aminoAcidSpecificity != null && !aminoAcidSpecificity
    2668             .equals(""))
    2669           {
    2670             String peptideSequence = fetchPeptideSequenceFromHitDescription(currentHit);
    2671             log.debug("peptideSequence = " + peptideSequence);
    2672             if (peptideSequence != null && !peptideSequence
    2673               .equals(""))
    2674             {
    2675               if (peptideSequence.contains(aminoAcidSpecificity))
    2676               {
    2677                 String userParamStr = new String(
    2678                   "userParam name=\"" + nameStr + "\" value=\"" + valueStr + "\" ");
    2679                 log.debug("peakListFile = " + peakListFile + " userParamStr = \"" + userParamStr + "\"");
    2680                 // Write modification userParam
    2681                 writeUserParam(xmlCrudeWriterImpl, userParamStr);
    2682               }
    2683             }
    2684           }
    2685           // Write modification PRIDE userParam for variable
    2686           // modification if peptide description supports it
    2687           List<String> peptideModTargetList = fetchPeptideModificationTargetListFromHitDescription(currentHit);
    2688           log.debug("peptideModTargetList = " + peptideModTargetList);
    2689           if (isVariable && peptideModTargetList != null && peptideModTargetList
    2690             .size() > 0)
    2691           {
    2692             String peptideModTarget = peptideModTargetList.get(0);
    2693             log.debug("peptideModTarget = " + peptideModTarget);
    2694             if (peptideModTarget != null && !peptideModTarget
    2695               .equals(""))
    2696             {
    2697               String userParamStr = new String(
    2698                 "userParam name=\"" + nameStr + "\" value=\"" + valueStr + "\" ");
    2699               log.debug("peakListFile = " + peakListFile + " userParamStr = \"" + userParamStr + "\"");
    2700               // Write modification cvParam
    2701               writeUserParam(xmlCrudeWriterImpl, userParamStr);
    2702             }
    2703           }
    2704         }
    2705       }
    2706     }
    2707   }
    27082427
    27092428
    … …  
    28412560
    28422561
    2843   /**
    2844    * Fetches peptide search engine string for search hit. Returns null if
    2845    * current hit is not a peptide hit.
    2846    *
    2847    * @param currentHit Hit The hit instance to get info from.
    2848    * @return String The search engine type, or null.
    2849    */
    2850   private String fetchPeptideSearchEngine(Hit currentHit)
    2851   {
    2852     String searchEngine = null;
    2853     // Check if peptide item (not protein)
    2854     log.debug("currentHit.isProtein() = " + currentHit.isProtein());
    2855     if (currentHit.isProtein() != null && !currentHit.isProtein())
    2856     {
    2857       //
    2858       // Get information from hit description
    2859       String scoreType = currentHit.getScoreType();
    2860       log.debug("scoreType = \"" + scoreType + "\"");
    2861       // For reporting purposes, get a simple search engine name
    2862       searchEngine = new String("Unknown search engine");
    2863       if (scoreType != null)
    2864       {
    2865         // Mascot
    2866         if (scoreType.startsWith("Mascot"))
    2867         {
    2868           searchEngine = new String("Mascot");
    2869         }
    2870         // X!Tandem
    2871         else if (scoreType.startsWith("Tandem"))
    2872         {
    2873           searchEngine = new String("Tandem");
    2874         }
    2875         // OMSSA
    2876         else if (scoreType.startsWith("OMSSA"))
    2877         {
    2878           searchEngine = new String("OMSSA");
    2879         }
    2880         // PIUMS
    2881         else if (scoreType.startsWith("PIUMS"))
    2882         {
    2883           searchEngine = new String("PIUMS");
    2884         }
    2885       }
    2886     }
    2887     log.debug("searchEngine = \"" + searchEngine + "\"");
    2888     return searchEngine;
    2889   }
    2890 
    2891 
    2892   /**
    2893    * Fetches peptide sequence string for search hit.
    2894    *
    2895    * @param currentHit Hit The hit instance to get info from.
    2896    * @return String The peptide sequence one-letter amino acid codes, or null.
    2897    */
    2898   private String fetchPeptideSequenceFromHitDescription(Hit currentHit)
    2899   {
    2900     String peptideSequence = null;
    2901     // Check if peptide item (not protein)
    2902     log.debug("currentHit.isProtein() = " + currentHit.isProtein());
    2903     if (currentHit.isProtein() != null && !currentHit.isProtein())
    2904     {
    2905       // Extract possible sequence string from hit description
    2906       String possibleSequence = null;
    2907       log.debug("currentHit.getDescription() = \"" + currentHit
    2908         .getDescription() + "\"");
    2909       String peptideDescription = currentHit.getDescription();
    2910       // Extract hit description string before first space
    2911       int spaceIndex = peptideDescription.indexOf(" ");
    2912       if (spaceIndex >= 0)
    2913       {
    2914         // Use description part before first space as sequence
    2915         possibleSequence = peptideDescription.substring(0, spaceIndex);
    2916       }
    2917       else
    2918       {
    2919         possibleSequence = peptideDescription;
    2920       }
    2921       log.debug("possibleSequence = \"" + possibleSequence + "\"");
    2922       // Check that peptide sequence consists of amino acid single letter
    2923       // codes
    2924       boolean isPossibleSequence = false;
    2925       if (possibleSequence
    2926         .matches("[G,A,L,M,F,W,K,Q,E,S,P,V,I,C,Y,H,R,N,D,T]*"))
    2927       {
    2928         log.debug("Peptide sequence string consists of single letter codes for the basic 20 amino acids.");
    2929         isPossibleSequence = true;
    2930       }
    2931       else if (possibleSequence
    2932         .matches("[G,A,L,M,F,W,K,Q,E,S,P,V,I,C,Y,H,R,N,D,T,B,Z,J,X]*"))
    2933       {
    2934         log.debug("Peptide sequence string consists of single letter codes for the basic 20 amino acids + [B,Z,J,X].");
    2935         isPossibleSequence = true;
    2936       }
    2937       log.debug("isPossibleSequence = " + isPossibleSequence);
    2938       if (isPossibleSequence)
    2939       {
    2940         peptideSequence = possibleSequence;
    2941       }
    2942     }
    2943     log.debug("peptideSequence = " + peptideSequence);
    2944     return peptideSequence;
    2945   }
    2946 
    2947 
    2948   /**
    2949    * Fetches peptide modification target string list for search hit.
    2950    *
    2951    * @param currentHit Hit The hit instance to get info from.
    2952    * @return String The peptide modification target string list without
    2953    *         multiplier, or null.
    2954    */
    2955   private List<String> fetchPeptideModificationTargetListFromHitDescription(
    2956       Hit currentHit)
    2957   {
    2958     List<String> modificationTargetList = null;
    2959     // Check if peptide item (not protein)
    2960     log.debug("currentHit.isProtein() = " + currentHit.isProtein());
    2961     if (currentHit.isProtein() != null && !currentHit.isProtein())
    2962     {
    2963       String searchEngine = fetchPeptideSearchEngine(currentHit);
    2964       // Mascot
    2965       if (searchEngine.equals("Mascot"))
    2966       {
    2967         String peptideDescription = currentHit.getDescription();
    2968         String peptideModification = null;
    2969         // Extract hit description string after first space
    2970         int spaceIndex = peptideDescription.indexOf(" ");
    2971         if (spaceIndex >= 0)
    2972         {
    2973           // Use description part after first space as modification
    2974           // string
    2975           if (peptideDescription.length() > spaceIndex)
    2976           {
    2977             peptideModification = peptideDescription
    2978               .substring(spaceIndex + 1);
    2979           }
    2980         }
    2981         log.debug("peptideModification = \"" + peptideModification + "\"");
    2982         if (peptideModification != null)
    2983         {
    2984           // Check for modification multiplier (integer space
    2985           // anything) "2 Oxidation (M)"
    2986           String modificationType = peptideModification;
    2987           if (peptideModification.matches("^\\d*\\ .*"))
    2988           {
    2989             // Extract multiplier before first space
    2990             spaceIndex = peptideModification.indexOf(" ");
    2991             if (spaceIndex >= 0)
    2992             {
    2993               // Use modification part after first space as
    2994               // modification string
    2995               if (peptideModification.length() > spaceIndex)
    2996               {
    2997                 modificationType = peptideModification
    2998                   .substring(spaceIndex + 1);
    2999               }
    3000             }
    3001           }
    3002           log.debug("modificationType = \"" + modificationType + "\"");
    3003           // Check for modification target (anything space
    3004           // left-parenthesis one-letter-amino-acid-codes
    3005           // right-parenthesis) "Oxidation (M)"
    3006           String modificationTarget = null;
    3007           if (modificationType
    3008             .matches("^.*\\ \\([G,A,L,M,F,W,K,Q,E,S,P,V,I,C,Y,H,R,N,D,T,B,Z,J,X]*\\)"))
    3009           {
    3010             // Extract modification type before last space
    3011             spaceIndex = modificationType.lastIndexOf(" ");
    3012             if (spaceIndex >= 0)
    3013             {
    3014               // Use modification part inside last parenthesis as
    3015               // modification target
    3016               if (modificationType.length() > (spaceIndex + 1))
    3017               {
    3018                 // Extract part after last " ("
    3019                 modificationTarget = modificationType
    3020                   .substring(spaceIndex + 2);
    3021                 // Remove last ")"
    3022                 if (modificationTarget.length() > 0)
    3023                 {
    3024                   modificationTarget = modificationTarget
    3025                     .substring(0,
    3026                       (modificationTarget.length() - 1));
    3027                 }
    3028               }
    3029               // Extract modification type before last space
    3030               modificationType = modificationType.substring(0,
    3031                 spaceIndex);
    3032             }
    3033           }
    3034           log.debug("modificationType = \"" + modificationType + "\" modificationTarget = \"" + modificationTarget + "\"");
    3035           // Construct modification target list
    3036           modificationTargetList = new ArrayList<String>();;
    3037           if (modificationTarget != null && modificationTarget
    3038             .length() > 0)
    3039           {
    3040             for (int i = 0; i < modificationTarget.length(); i++)
    3041             {
    3042               // Add amino acid one-letter code #i to list
    3043               String code = modificationTarget
    3044                 .substring(i, i + 1);
    3045               modificationTargetList.add(code);
    3046             }
    3047           }
    3048           log.debug("modificationType = \"" + modificationType + "\" modificationTargetList = " + modificationTargetList);
    3049         }
    3050       }
    3051     }
    3052     log.debug("modificationTargetList = " + modificationTargetList);
    3053     return modificationTargetList;
    3054   }
    30552562
    30562563
    … …  
    30882595
    30892596
    3090   /**
    3091    * Write cvParam string
    3092    *
    3093    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    3094    *        XMLCrudeWriterImpl to use.
    3095    * @param cvParamStr String The cvParam string to write.
    3096    */
    3097   private void writeCvParam(XMLCrudeWriter xmlCrudeWriterImpl,
    3098       String cvParamStr)
    3099   {
    3100     // Write cvParam
    3101     writeSingleTag(xmlCrudeWriterImpl, cvParamStr);
    3102   }
    3103 
    3104 
    3105   /**
    3106    * Write userParam string
    3107    *
    3108    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    3109    *        XMLCrudeWriterImpl to use.
    3110    * @param userParamStr String The userParam string to write.
    3111    */
    3112   private void writeUserParam(XMLCrudeWriter xmlCrudeWriterImpl,
    3113       String userParamStr)
    3114   {
    3115     // Write userParam
    3116     writeSingleTag(xmlCrudeWriterImpl, userParamStr);
    3117   }
    3118 
    3119 
    3120   /**
    3121    * Write single XML tag
    3122    *
    3123    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    3124    *        XMLCrudeWriterImpl to use.
    3125    * @param content String The tag string content to write.
    3126    */
    3127   private void writeSingleTag(XMLCrudeWriter xmlCrudeWriterImpl,
    3128       String content)
    3129   {
    3130     if (content != null)
    3131     {
    3132       // Write single XML tag
    3133       try
    3134       {
    3135         xmlCrudeWriterImpl.writeStartElement(content);
    3136         xmlCrudeWriterImpl.writeSingleElementEnd();
    3137       }
    3138       catch (XMLStreamException e)
    3139       {
    3140         log.warn("Problem when generating xml file " + xmlFilePath + " : " + e);
    3141       }
    3142     }
    3143   }
    31442597
    31452598
    … …  
    35703023  }
    35713024
    3572 
    3573   /**
    3574    * Copy selected XML block from source XML file to XML output.
    3575    *
    3576    * @param dc DbControl The DbControl to use.
    3577    * @param xmlCrudeWriterImpl XMLCrudeWriterImpl Instance of
    3578    *        XMLCrudeWriterImpl to use.
    3579    * @param sourceFileId Integer Database id of source file item with XML
    3580    *        input.
    3581    * @param selectedXmlTagName String Name of selected XML tag.
    3582    * @param firstLineExtraIndentation int Extra indentation steps for first
    3583    *        line.
    3584    * @throws XMLStreamException If there is an XML Stream related error
    3585    */
    3586   private void copySelectedXMLBlocks(DbControl dc,
    3587       XMLCrudeWriter3Impl xmlCrudeWriterImpl, Integer sourceFileId,
    3588       String selectedXmlTagName, String selectedXMLEndTag,
    3589       int firstLineExtraIndentation)
    3590       throws XMLStreamException
    3591   {
    3592     copySelectedXMLBlocks(dc, xmlCrudeWriterImpl, sourceFileId,
    3593       selectedXmlTagName, selectedXMLEndTag, false,
    3594       firstLineExtraIndentation);
    3595   }
    35963025
    35973026
    … …  
    38263255
    38273256
    3828   /**
    3829    * Writes XML start tag for an XML block.
    3830    *
    3831    * @param String tag name
    3832    * @throws XMLStreamException If there is an XML Stream related error
    3833    */
    3834   private void writeStartTag(String tagName)
    3835       throws XMLStreamException
    3836   {
    3837     /*
    3838      * Write start tag for ant XML block.
    3839      */
    3840     xmlCrudeWriter.writeStartElement(tagName);
    3841     xmlCrudeWriter.writeStartElementEnd();
    3842   }
    3843 
    3844 
    3845   /**
    3846    * Writes XML end tag for an XML block.
    3847    *
    3848    * @param String tag name
    3849    * @throws XMLStreamException If there is an XML Stream related error
    3850    */
    3851   private void writeEndTag(String tagName)
    3852       throws XMLStreamException
    3853   {
    3854     /*
    3855      * Write end tag for current XML block.
    3856      */
    3857     xmlCrudeWriter.writeEndElement(tagName);
    3858   }
    38593257
    38603258
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