Changeset 3778

Timestamp:

Aug 18, 2010, 3:18:04 PM (13 years ago)

Author:

Fredrik Levander

Message:

Only querying for peptides

File:

• trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java (modified) (4 diffs)

trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java

@@ -1 @@
-
 package satoshi;
 
@@ -433 +432 @@
       hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"),
         Hql.entity(project)));
+      hitQuery.restrictPermanent(Restrictions.eq(Hql.property("protein"),
+        Expressions.parameter("protein")));
+      hitQuery.setPermanentParameter("protein", false, null);
       hitQuery.restrict(Restrictions.lteq(Hql.property("combinedFDR"),
         Expressions.aFloat((float) fdrCutOff)));
@@ -446 +448 @@
       {
         Hit currentHit = hitit.next();
-        if (!currentHit.isProtein())
-        {
-          if (hitit.hasNext())
-          {
-            // log.debug(">" + pklFile + "\t" + output + "\t" +
-            // output2 + "\t" + peptidelist + "\n");
-            if (pklFile != null && currentHit.getPeakListFile() != pklFile)
-            {
-              // start retrieving all necessary info.
-              // including spectrum for each hit
-              retrieveMZAndTotalIntensity(pklFile, hitList,
-                output, output2, dc);
-              // empty hitList and store the currentHit
-              hitList.clear();
-              hitList.add(currentHit);
-              pklFile = currentHit.getPeakListFile();
-            }
-            else
-            {
-              hitList.add(currentHit);
-              pklFile = currentHit.getPeakListFile(); // get the
-              // file name
-              // even if it is the same as before
-            }
-          }
-          else
-          {
-            // log.debug(">2" + pklFile + "\t" + output + "\t" +
-            // output2 + "\t" + peptidelist + "\n");
+        if (hitit.hasNext())
+        {
+          // log.debug(">" + pklFile + "\t" + output + "\t" +
+          // output2 + "\t" + peptidelist + "\n");
+          if (pklFile != null && currentHit.getPeakListFile() != pklFile)
+          {
+            // start retrieving all necessary info.
+            // including spectrum for each hit
             retrieveMZAndTotalIntensity(pklFile, hitList, output,
               output2, dc);
+            // empty hitList and store the currentHit
             hitList.clear();
             hitList.add(currentHit);
-          }
+            pklFile = currentHit.getPeakListFile();
+          }
+          else
+          {
+            hitList.add(currentHit);
+            pklFile = currentHit.getPeakListFile(); // get the
+            // file name
+            // even if it is the same as before
+          }
+        }
+        else
+        {
+          // log.debug(">2" + pklFile + "\t" + output + "\t" +
+          // output2 + "\t" + peptidelist + "\n");
+          retrieveMZAndTotalIntensity(pklFile, hitList, output,
+            output2, dc);
+          hitList.clear();
+          hitList.add(currentHit);
         }
       }
@@ -684 +683 @@
       List<Integer> requestSpectraCharge = new ArrayList<Integer>();
       List<String> requestSpectraStartPosition = new ArrayList<String>();
-      DecimalFormatSymbols dfs =  new DecimalFormatSymbols(Locale.US);
-      DecimalFormat fourDecimals = new DecimalFormat("####.0000",dfs);
+      DecimalFormatSymbols dfs = new DecimalFormatSymbols(Locale.US);
+      DecimalFormat fourDecimals = new DecimalFormat("####.0000", dfs);
       // correct only unique ones
       int requestSpectraNr = 0;
       for (Hit phit : peptideHits)
       {
-        // ignore proteins
-        if (!phit.isProtein())
-        {
-          // make sure the file format and its interface
-          if (!requestSpectraStringID.contains(phit
-            .getSpectrumStringId()))
-          {
-            requestSpectraStringID.add(phit.getSpectrumStringId());
-            String[] s1 = phit.getDescription().split(" ", 2);
-            requestSpectraSEQ.add(s1[0]); // sequence
-            if (s1.length == 2)
+        // make sure the file format and its interface
+        if (!requestSpectraStringID
+          .contains(phit.getSpectrumStringId()))
+        {
+          requestSpectraStringID.add(phit.getSpectrumStringId());
+          String[] s1 = phit.getDescription().split(" ", 2);
+          requestSpectraSEQ.add(s1[0]); // sequence
+          if (s1.length == 2)
+          {
+            requestSpectraModification.add(s1[1]); // modification
+            // if any
+            // log.debug(">" + s1[0] + "\t" + s1[1]);
+          }
+          else
+          {
+            requestSpectraModification.add(null); // put
+            // something
+            // so that
+            // the order
+            // is kept
+            // log.debug(">" + s1[0] + "\n");
+          }
+          // expectation value
+          requestSpectraEXP.add(phit.getExpectationValue());
+          // combinedFDR
+          requestSpectraFDR.add(phit.getCombinedFDR());
+          // experimental mass
+          requestSpectraExperimentalMassD.add(phit
+            .getExperimentalMassInDaltons());
+          // delta mass
+          requestSpectraDeltaMassD.add(phit.getDeltaMassInDaltons());
+          // charge
+          requestSpectraCharge.add(phit.getCharge());
+
+          // IPI IDs and get the appropriate Peptide for
+          // positional info for each hit
+          requestSpectraPeaklistFileName.add(phit.getPeakListFile());
+          String[] s2 = phit.getExternalId().split(",");
+
+          // Start positions
+          String id = null;
+          List<String> idlist = new ArrayList<String>();
+          if (mgfFormat)
+          {
+            for (int i = 0; i < s2.length; i++)
             {
-              requestSpectraModification.add(s1[1]); // modification
-              // if any
-              // log.debug(">" + s1[0] + "\t" + s1[1]);
+              String id2 = s2[i] + "@" + getStartPosition(s2[i],
+                phit.getDescription(), dc);
+              idlist.add(id2);
+              id = id2;
             }
-            else
-            {
-              requestSpectraModification.add(null); // put
-              // something
-              // so that
-              // the order
-              // is kept
-              // log.debug(">" + s1[0] + "\n");
-            }
-            // expectation value
-            requestSpectraEXP.add(phit.getExpectationValue());
-            // combinedFDR
-            requestSpectraFDR.add(phit.getCombinedFDR());
-            // experimental mass
-            requestSpectraExperimentalMassD.add(phit
-              .getExperimentalMassInDaltons());
-            // delta mass
-            requestSpectraDeltaMassD.add(phit
-              .getDeltaMassInDaltons());
-            // charge
-            requestSpectraCharge.add(phit.getCharge());
-
-            // IPI IDs and get the appropriate Peptide for
-            // positional info for each hit
-            requestSpectraPeaklistFileName.add(phit
-              .getPeakListFile());
-            String[] s2 = phit.getExternalId().split(",");
-
-            // Start positions
-            String id = null;
-            List<String> idlist = new ArrayList<String>();
-            if (mgfFormat)
-            {
-              for (int i = 0; i < s2.length; i++)
-              {
-                String id2 = s2[i] + "@" + getStartPosition(
-                  s2[i], phit.getDescription(), dc);
-                idlist.add(id2);
-                id = id2;
-              }
-            }
-            requestSpectraNr++;
-            log.debug("Retrieved startpos:" + requestSpectraNr);
-            // log.debug(">query begin\n");
-            // ItemQuery<Peptide> peptideQuery = Peptide.getQuery();
-            // peptideQuery.restrict(Restrictions.eq(Hql
-            // .property("sequence"), Expressions
-            // .parameter("sequence")));
-            // peptideQuery.setParameter("sequence", s1[0], null);
-            // peptideQuery.restrict(Restrictions.eq(Hql
-            // .property("accessionNumber"), Expressions
-            // .parameter("accessionNumber")));
-            // peptideQuery.setParameter("accessionNumber", ipi,
-            // null);
-
-            // ItemResultIterator<Peptide> pepit =
-            // peptideQuery.iterate(dc);
-            // if (pepit.hasNext())
-            // {
-            // String id2 = ipi + "@" +
-            // pepit.next().getStartPosition();
-            // idlist.add(id2);
-            // id = id2;
-            // }
-            // log.debug(">query end\n");
-
-            requestSpectraExternalID.add(idlist);
-          }
+          }
+          requestSpectraNr++;
+          log.debug("Retrieved startpos:" + requestSpectraNr);
+          // log.debug(">query begin\n");
+          // ItemQuery<Peptide> peptideQuery = Peptide.getQuery();
+          // peptideQuery.restrict(Restrictions.eq(Hql
+          // .property("sequence"), Expressions
+          // .parameter("sequence")));
+          // peptideQuery.setParameter("sequence", s1[0], null);
+          // peptideQuery.restrict(Restrictions.eq(Hql
+          // .property("accessionNumber"), Expressions
+          // .parameter("accessionNumber")));
+          // peptideQuery.setParameter("accessionNumber", ipi,
+          // null);
+
+          // ItemResultIterator<Peptide> pepit =
+          // peptideQuery.iterate(dc);
+          // if (pepit.hasNext())
+          // {
+          // String id2 = ipi + "@" +
+          // pepit.next().getStartPosition();
+          // idlist.add(id2);
+          // id = id2;
+          // }
+          // log.debug(">query end\n");
+
+          requestSpectraExternalID.add(idlist);
         }
       }