Changeset 3777

Timestamp:

Aug 18, 2010, 2:43:02 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #614. Adding link to feature peptide sequences, to find the matching hits.

Location:

trunk/client/servlet/src

Files:

• locale/en/dictionary (modified) (8 diffs)
• org/proteios/action/ActionFactory.java (modified) (4 diffs)
• org/proteios/action/feature/FeatureHitMatchForm.java (modified) (4 diffs)
• org/proteios/action/feature/ViewFeatureHits.java (added)

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

@@ -153 +153 @@
 EndDate=End Date
 Ended=Ended
+EndTimeToleranceMinutes=End retention time tolerance (min)
 EndRetentionTimeInMinutes=End retention time (min)
 EnterContactData=Enter Contact Data
@@ -191 +192 @@
 Extracts=Extracts
 FastJobQueue=Fast
+Feature=Feature
 FeatureExternalId=Feature External ID
 FeatureFile=Feature File
@@ -304 +306 @@
 isNotADirectory=is not a directory
 IsNotADirectory=is not a directory
+isSecondary=Match related
 itemDeleted=item deleted
 ItemId=Item ID
@@ -391 +394 @@
 MassToChargeRatio = m/z
 MatchedPeaks=Matched Peaks
-MatchFeatureHits=Match features and hits
+MatchFeaturesHits=Match features and hits
 MaxNumMissedCleavages=Max Number of Missed Cleavages
 Md5=MD5
@@ -413 +416 @@
 MzDataFile=mzData File
 MzMLFile=mzML File
+MzTolerance=m/z tolerance
 Name=Name
 NewDirectory=New directory
@@ -601 +605 @@
 PoolExtracts=Pool Extracts
 Precursor=Precursor
+PrecursorQuantity=Precursor quantity
 PreferencesMenuItem=Preferences...
 Preferences=Preferences
@@ -707 +712 @@
 ScoreType=Score Type
 ScoreTypeSettings=Settings for score type
+Search=Search
 SearchDatabases=Search database(s)
 SearchDate=Searched
@@ -800 +806 @@
 StartHere=Start Here
 StartRetentionTimeInMinutes=Start retention time (min)
+StartTimeToleranceMinutes=Start retention time tolerance (min)
 Start=Start
 StatusMessage=Status Message

trunk/client/servlet/src/org/proteios/action/ActionFactory.java

@@ -41 +41 @@
 import org.proteios.action.execute.Login;
 import org.proteios.action.extract.ViewExtract;
+import org.proteios.action.feature.ViewFeatureHits;
 import org.proteios.action.file.ViewFile;
 import org.proteios.action.gel.ViewGelOrNewGel;
@@ -50 +51 @@
 import org.proteios.action.hit.ViewHitSpectrumFile;
 import org.proteios.action.hit.ViewHitSubHits;
+import org.proteios.action.job.ViewJob;
 import org.proteios.action.news.ViewNews;
-import org.proteios.action.job.ViewJob;
 import org.proteios.action.plugin.ViewPluginDefinition;
 import org.proteios.action.project.ViewProject;
-import org.proteios.action.project.ViewProjectHome;
 import org.proteios.action.read.ViewHome;
 import org.proteios.action.sample.ViewSample;
@@ -65 +65 @@
 import org.proteios.core.ItemFactory;
 import org.proteios.core.ItemNotFoundException;
+import org.proteios.core.Job;
+import org.proteios.core.News;
 import org.proteios.core.PermissionDeniedException;
-import org.proteios.core.Job;
 import org.proteios.core.PluginDefinition;
 import org.proteios.core.Project;
 import org.proteios.core.QueryFactory;
 import org.proteios.core.Sample;
-import org.proteios.core.News;
 import org.proteios.core.SessionControl;
 import org.proteios.core.User;
@@ -645 +645 @@
       }
     }
+    if (describedClass.equals(org.proteios.core.Feature.class))
+    {
+      if (key.equals("PeptideSequence"))
+      {
+        link = getActionLink(ViewFeatureHits.class, label);
+      }
+    }
     if (describedClass.equals(Hit.class))
     {

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

@@ -35 +35 @@
     ColumnContainer cc;
     cc = new ColumnContainer();
-    title = new Title("FeatureHitsMatchForm");
+    title = new Title("Settings for matching features and MS/MS identifications");
     Form form = new Form("FeatureHitsMatchForm");
     Fieldset properties = new Fieldset();
@@ -43 +43 @@
       CreateFeatureHitMatchJob.VTOLERANCE);
     tolF.setValue(new Float(0.01));
-    tolF.setLabel("Tolerance");
+    tolF.setLabel("MzTolerance");
     properties.add(tolF);
     TextField<Float> tolStartF = new TextField<Float>(
@@ -49 +49 @@
     tolStartF.setValue(new Float(0.5));
     tolStartF.setLabel("StartTimeToleranceMinutes");
+    tolStartF.setHelp("MS/MS before feature start retention time.");
     properties.add(tolStartF);
     TextField<Float> tolEndF = new TextField<Float>(
@@ -54 +55 @@
     tolEndF.setValue(new Float(0.5));
     tolEndF.setLabel("EndTimeToleranceMinutes");
+    tolEndF.setHelp("MS/MS after feature end retention time.");
     properties.add(tolEndF);
     Checkbox<VBoolean> isSecondaryF = new Checkbox<VBoolean>(