X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=c71818e2dae8ab46be141ffdf76a1507b99a0e2a;hb=8a3c31b03ed98321d1d450b658d26d50a7aa0ae6;hp=b45fa6b45e051704d94ca6e18ac02a550de7d9c3;hpb=b4877bc99e12cf4465e43e090e19277c3139ce77;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b45fa6b..c71818e 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -28,6 +28,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.util.UrlLink;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.SequenceAnnotationReport;
 
 public class APopupMenu extends java.awt.PopupMenu implements
         ActionListener, ItemListener
@@ -108,15 +109,21 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem editSequence = new MenuItem("Edit Sequence");
 
+  MenuItem sequenceDetails = new MenuItem("Sequence Details ...");
+
+  MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
+
   Sequence seq;
 
   MenuItem revealAll = new MenuItem();
 
   MenuItem revealSeq = new MenuItem();
+
   /**
    * index of sequence to be revealed
    */
-  int revealSeq_index=-1;
+  int revealSeq_index = -1;
+
   Menu menu1 = new Menu();
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
@@ -152,7 +159,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (sg != null && sg.getSize() > 0)
     {
-      editGroupName.setLabel("Name: "+sg.getName());
+      editGroupName.setLabel("Name: " + sg.getName());
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
@@ -185,7 +192,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         final String target = urlLink.getTarget(); // link.substring(0,
         // link.indexOf("|"));
         final String label = urlLink.getLabel();
-        if (seq!=null && urlLink.isDynamic())
+        if (seq != null && urlLink.isDynamic())
         {
 
           // collect matching db-refs
@@ -304,14 +311,18 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       remove(revealAll);
       remove(revealSeq);
-    } else {
+    }
+    else
+    {
       final int index = ap.av.getAlignment().findIndex(seq);
 
       if (ap.av.adjustForHiddenSeqs(index)
               - ap.av.adjustForHiddenSeqs(index - 1) > 1)
       {
-        revealSeq_index=index;
-      } else {
+        revealSeq_index = index;
+      }
+      else
+      {
         remove(revealSeq);
       }
     }
@@ -450,6 +461,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       editName();
     }
+    else if (source == sequenceDetails)
+    {
+      showSequenceDetails();
+    }
+    else if (source == selSeqDetails)
+    {
+      showSequenceSelectionDetails();
+    }
     else if (source == pdb)
     {
       addPDB();
@@ -514,7 +533,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
                   EditCommand.REPLACE, dialog.getName().replace(' ',
                           ap.av.getGapCharacter()),
                   sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
-                  sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
+                  sg.getStartRes(), sg.getEndRes() + 1,
+                  ap.av.getAlignment());
 
           ap.alignFrame.addHistoryItem(editCommand);
 
@@ -529,8 +549,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       Vector regions = new Vector();
       if (sg != null)
       {
-        int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
-                sg.getEndRes() + 1);
+        int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+                sg.getStartRes(), sg.getEndRes() + 1);
 
         String description;
         int caseChange;
@@ -552,8 +572,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
         }
 
         ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
-                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
-                caseChange);
+                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+                startEnd, caseChange);
 
         ap.alignFrame.addHistoryItem(caseCommand);
 
@@ -616,7 +636,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
             "Selection output - " + e.getActionCommand(), 600, 500);
-    // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
+    // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
+    // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
@@ -626,6 +647,46 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   }
 
+  protected void showSequenceSelectionDetails()
+  {
+    createSequenceDetailsReport(ap.av.getSequenceSelection());
+  }
+
+  protected void showSequenceDetails()
+  {
+    createSequenceDetailsReport(new SequenceI[]
+    { seq });
+  }
+
+  public void createSequenceDetailsReport(SequenceI[] sequences)
+  {
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+    StringBuffer contents = new StringBuffer();
+    for (SequenceI seq : sequences)
+    {
+      contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
+              + "</h2></p><p>");
+      new SequenceAnnotationReport(null)
+              .createSequenceAnnotationReport(
+                      contents,
+                      seq,
+                      true,
+                      true,
+                      false,
+                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                              : null);
+      contents.append("</p>");
+    }
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+            + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+                    : "Selection"), 600, 500);
+    cap.setText("<html>" + contents.toString() + "</html>");
+  }
+
   void editName()
   {
     EditNameDialog dialog = new EditNameDialog(seq.getName(),
@@ -662,7 +723,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       cap.setPDBImport(seq);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+seq.getName(), 400, 300);
+      jalview.bin.JalviewLite.addFrame(frame,
+              "Paste PDB file for sequence " + seq.getName(), 400, 300);
     }
   }
 
@@ -685,6 +747,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     showBoxes.setState(true);
     showBoxes.addItemListener(this);
     sequenceName.addActionListener(this);
+    sequenceDetails.addActionListener(this);
+    selSeqDetails.addActionListener(this);
     displayNonconserved.setLabel("Show Nonconserved");
     displayNonconserved.setState(false);
     displayNonconserved.addItemListener(this);
@@ -705,6 +769,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     this.add(hideSeqs);
     this.add(revealSeq);
     this.add(revealAll);
+    // groupMenu.add(selSeqDetails);
     groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
@@ -771,6 +836,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     toLower.addActionListener(this);
     editMenu.add(toggleCase);
     seqMenu.add(sequenceName);
+    // seqMenu.add(sequenceDetails);
+
     if (!ap.av.applet.useXtrnalSviewer)
     {
       seqMenu.add(pdb);
@@ -798,9 +865,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            ap.av.getAlignment().getWidth());
+    sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
     refresh();
   }
 
@@ -862,9 +927,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
-              ap.av.getAlignment().getWidth()));
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+              .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
@@ -892,9 +956,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.getHiddenRepSequences()), 0,
-            ap.av.getAlignment().getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+            .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
     refresh();
   }
 
@@ -904,9 +967,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.getHiddenRepSequences()), 0,
-            ap.av.getAlignment().getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+            .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
 
     refresh();
   }
@@ -929,10 +991,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
 
       sg.cs.setConservation(Conservation.calculateConservation("Group",
-              ResidueProperties.propHash, 3,
-              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
-              ap.av.getAlignment().getWidth(),
-              false, ap.av.getConsPercGaps(),false));
+              ResidueProperties.propHash, 3, sg.getSequences(ap.av
+                      .getHiddenRepSequences()), 0, ap.av.getAlignment()
+                      .getWidth(), false, ap.av.getConsPercGaps(), false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }