Changeset 4539

Timestamp:

Dec 20, 2013, 10:14:06 AM (9 years ago)

Author:

Fredrik Levander

Message:

Refs #821.

Location:

trunk

Files:

• client/servlet/src/locale/en/dictionary (modified) (2 diffs)
• client/servlet/src/org/proteios/action/feature/CreateFeatureComparisonJob.java (modified) (5 diffs)
• client/servlet/src/org/proteios/action/feature/FeatureComparisonForm.java (modified) (3 diffs)
• plugin/src/org/proteios/plugins/FeatureComparison.java (modified) (8 diffs)

trunk/client/servlet/src/locale/en/dictionary

@@ -298 +298 @@
 IdentificationResultFile=Search results file
 Id=ID
+IdentifiedOnly=Identified Only
 ImportedPeakLists=Imported Peak Lists
 ImportedSearches=Imported Searches
@@ -455 +456 @@
 MimeType=MIME Type
 MinPep=Minimum peptides
+MinSamples=Minimum samples
 MissingFile=Missing File
 Model=Model

trunk/client/servlet/src/org/proteios/action/feature/CreateFeatureComparisonJob.java

@@ -30 +30 @@
 import org.proteios.action.ProteiosAction;
 import org.proteios.action.job.ListJobs;
+import org.proteios.core.BooleanParameterType;
 import org.proteios.core.DbControl;
+import org.proteios.core.IntegerParameterType;
 import org.proteios.core.ItemFactory;
 import org.proteios.core.ItemParameterType;
@@ -40 +42 @@
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VBoolean;
+import se.lu.thep.waf.constraints.VInteger;
 import se.lu.thep.waf.constraints.VString;
 
@@ -50 +54 @@
 
   public static final VString VFILENAME = new VString("name", 1, 100, true);
+  public static final VInteger VMINSAMPLESWITHVALUES = new VInteger("minSamples", 0, 10000, true);
+  public static final VBoolean VIDENTIFIEDONLY = new VBoolean("isIdentifiedOnly", false);
   
   /*
@@ -67 +73 @@
     ItemFactory factory = getItemFactory(dc);
     String filename = getValidString(VFILENAME);
+    Integer minSamplesWithValues = getValidInteger(VMINSAMPLESWITHVALUES);
+    Boolean isIdentifiedOnly = getValidBoolean(VIDENTIFIEDONLY);
+    if (isIdentifiedOnly == null)
+      isIdentifiedOnly = new Boolean(false);
     /***********************************************************************
      * Create jobs
@@ -95 +105 @@
     // File parameters
     job.setParameterValue("filename", new StringParameterType(), filename);
+    job.setParameterValue("minSamplesWithValues", new IntegerParameterType(), minSamplesWithValues);
+    job.setParameterValue("identifiedOnly", new BooleanParameterType(),isIdentifiedOnly);
     job.setName("Compare features");
-    job.setDescription("Project:" + project+ ", outfile:"+filename);
+    job.setDescription("Project:" + project+ ", outfile:"+filename+", identified only:"+isIdentifiedOnly+", min samples with values:"+minSamplesWithValues);
     dc.saveItem(job);
     dc.commit();

trunk/client/servlet/src/org/proteios/action/feature/FeatureComparisonForm.java

@@ -10 +10 @@
 import org.proteios.gui.Title;
 import org.proteios.gui.Toolbar;
+import org.proteios.gui.form.Checkbox;
 import org.proteios.gui.form.Fieldset;
 import org.proteios.gui.form.Form;
@@ -17 +18 @@
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VBoolean;
 
 import java.util.ArrayList;
@@ -44 +46 @@
     nameF.setLabel("OutputFileName");
     properties.add(nameF);
+    TextField<Integer> minF = new TextField<Integer>(
+        CreateFeatureComparisonJob.VMINSAMPLESWITHVALUES);
+    minF.setValue(new Integer(1));
+    minF.setLabel("MinSamples");
+    minF.setHelp("Only report feature with values in at least this number of samples");
+    properties.add(minF);
+    Checkbox<VBoolean> isIdentifiedOnly = new Checkbox<VBoolean>(
+        CreateFeatureComparisonJob.VIDENTIFIEDONLY);
+    isIdentifiedOnly.setLabel("IdentifiedOnly");
+    isIdentifiedOnly.setValue("true");
+    isIdentifiedOnly
+        .setHelp("Check to only report features with assigned peptides sequence.");
+    properties.add(isIdentifiedOnly);
+
     Toolbar tb = new Toolbar();
     form.setToolbar(tb);

trunk/plugin/src/org/proteios/plugins/FeatureComparison.java

@@ -65 +65 @@
 
 /**
- * This analysis plugin will create a hits comparison report.
+ * This plugin will create a feature report.
  * 
  * @author olle
@@ -79 +79 @@
 
   private Map<String, FeatureRow> valueMap = new TreeMap<String, FeatureRow>();
-
+    private Integer minSamples = 1;
+    private Boolean identifiedOnly = false;
 
   public MainType getMainType()
@@ -90 +91 @@
   {
     return new AboutImpl("Feature Comparison Report",
-      "Generate table with feature comparison", "0.2",
+      "Generate table with feature comparison", "0.3",
       "2012-2103, Immunotechnology, Lund University", null, null,
       "http://www.proteios.org  ");
@@ -118 +119 @@
       String filenamePrefix = (String) job.getValue("filename");
       log.debug("filenamePrefix = \"" + filenamePrefix + "\"");
+      minSamples = (Integer) job.getValue("minSamplesWithValues");
+      identifiedOnly = ((Boolean) job.getValue("identifiedOnly")).booleanValue();
       ItemFactory factory = new ItemFactory(dc);
       File outCoreFile = factory.create(File.class);
@@ -131 +134 @@
       // Write report header
       writer.println("Feature Comparison Report");
-      writer.println("");
+      writer.println("Minimum samples with values:"+minSamples+". Only writing features with assigned identitites:"+identifiedOnly);
       writer
         .println("File generated by Proteios SE " + proteiosVersion + " build " + proteiosBuildNumber + " (" + timestamp + ")");
@@ -207 +210 @@
       if (!feature.getClusterId().equals(currentCluster))
       {
-        if (nEntries > 1)
+        if (nEntries >= 1)
         {
           treatRow(writer, values, currentCluster, currentSequence,
@@ -274 +277 @@
 
     }
-    treatRow(writer, values, currentCluster, currentSequence, currentAcc,
+    if (nEntries >= 1) treatRow(writer, values, currentCluster, currentSequence, currentAcc,
       currentCharge, rtSum, nValues, conflict);
     for (String key : valueMap.keySet())
@@ -344 +347 @@
       int currentCharge, float rtSum, float nValues, boolean conflict)
   {
-    if (values != null)
-    {
-      writer.print(currentCluster + "\t" + currentSequence);
-      if (conflict)
-        writer.print(",+");
-      writer
-        .print("\t" + currentAcc + "\t" + currentCharge + "\t" + (rtSum / nValues));
-      for (Float value : values)
-      {
-        writer.print("\t" + value);
-      }
-      writer.println();
-    }
-
+    if (values != null && (!currentSequence.equals("") || !identifiedOnly))
+    {
+      int count=0;
+      for (Float v:values)
+      {
+        if (v!=null) count++;
+      }
+      if (count>=minSamples)
+      {
+        writer.print(currentCluster + "\t" + currentSequence);
+        if (conflict)
+          writer.print(",+");
+        writer
+          .print("\t" + currentAcc + "\t" + currentCharge + "\t" + (rtSum / nValues));
+        for (Float value : values)
+        {
+          writer.print("\t" + value);
+        }
+        writer.println();
+      }
+    }
   }