X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ccf7303f35160d152b5f9854d58296cc4b07c7fb;hb=b2319fcc38be5c500ed7cafc014cf9da96a4ce98;hp=3319b338db89f9b4e00ac3e7aa9b76941c884733;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3319b33..ccf7303 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -174,18 +174,13 @@ public class AlignFrame
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible( nucleotide );
-    sequenceFeatures.setVisible(!nucleotide );
-    featureSettings.setVisible( !nucleotide );
+    //sequenceFeatures.setVisible(!nucleotide );
+    //featureSettings.setVisible( !nucleotide );
     conservationMenuItem.setVisible( !nucleotide );
     modifyConservation.setVisible(   !nucleotide );
 
-    //Deal with separators
     //Remember AlignFrame always starts as protein
-    if(nucleotide)
-    {
-      viewMenu.remove(viewMenu.getItemCount()-2);
-    }
-    else
+    if(!nucleotide)
     {
       calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
@@ -205,8 +200,6 @@ public class AlignFrame
   {
     new SequenceFetcher(this);
   }
-
-
   /**
    * DOCUMENT ME!
    *
@@ -270,7 +263,7 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);
       }
 
-      Jalview2XML.SaveAlignment(this, file, shortName);
+      new Jalview2XML().SaveAlignment(this, file, shortName);
 
       // USE Jalview2XML to save this file
       return true;
@@ -367,6 +360,27 @@ public class AlignFrame
     thread.start();
   }
 
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
+    }
+
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -457,42 +471,8 @@ public class AlignFrame
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
-    }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -698,7 +678,7 @@ public class AlignFrame
       if(str.length()<1)
         return;
 
-      String format = IdentifyFile.Identify(str, "Paste");
+      String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
      if(Desktop.jalviewClipboard!=null)
@@ -726,6 +706,10 @@ public class AlignFrame
         AlignFrame af = new AlignFrame(alignment);
         String newtitle = new String("Copied sequences");
 
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+
         if (title.startsWith("Copied sequences"))
         {
           newtitle = title;
@@ -810,24 +794,50 @@ public class AlignFrame
       return;
     }
 
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if (sg.sequences.size() == viewport.alignment.getHeight())
+
+
+
+    //Jalview no longer allows deletion of residues.
+    //Check here whether any residues are in selection area
+    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
-      allSequences = true;
+      for (int i = 0; i < sg.sequences.size(); i++)
+      {
+        SequenceI seq = sg.getSequenceAt(i);
+        int j = sg.getStartRes();
+        do
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+          {
+            JOptionPane.showInternalMessageDialog(
+                Desktop.desktop, "Cannot delete residues from alignment!\n"
+                + "Try hiding columns instead.",
+                "Deletion of residues not permitted",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+          j++;
+        }while(j<=sg.getEndRes());
+      }
     }
 
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
+
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
+      if (sg.sequences.size() == viewport.alignment.getHeight())
       {
         viewport.getColumnSelection().removeElements(sg.getStartRes(),
             sg.getEndRes() + 1);
@@ -902,12 +912,16 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
-    alignPanel.annotationPanel.activeRes = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -1125,7 +1139,10 @@ public class AlignFrame
 
  public void alignmentChanged()
  {
-   if(viewport.vconsensus!=null)
+   if(viewport.padGaps)
+     viewport.getAlignment().padGaps();
+
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
    {
      viewport.updateConsensus();
      viewport.updateConservation();
@@ -1187,8 +1204,11 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-    if (viewport.getAlignment().padGaps())
-      alignmentChanged();
+
+    viewport.padGaps = padGapsMenuitem.isSelected();
+
+   // if (viewport.padGaps)
+    alignmentChanged();
   }
 
   /**
@@ -1201,8 +1221,8 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
   }
 
   /**
@@ -1329,25 +1349,37 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+    if (!viewport.alignment.isNucleotide())
+    {
+      new SequenceFeatureFetcher(viewport.
+                                 alignment,
+                                 alignPanel);
+      viewport.setShowSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
+    }
+  }
+
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param evt DOCUMENT ME!
    */
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-
-    if (viewport.showSequenceFeatures)
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+    alignPanel.repaint();
+    if (alignPanel.getOverviewPanel() != null)
     {
-      new SequenceFeatureFetcher(viewport.
-         alignment,
-          alignPanel);
+      alignPanel.getOverviewPanel().updateOverviewImage();
     }
-
-    featureSettings.setEnabled(true);
-
-    alignPanel.repaint();
   }
 
   /**
@@ -1907,6 +1939,13 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1956,7 +1995,7 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 3))
@@ -2008,7 +2047,6 @@ public class AlignFrame
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2425,10 +2463,7 @@ public class AlignFrame
     }
   }*/
 
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
+
 
 
 
@@ -2445,6 +2480,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
     protein = new StringBuffer();
     seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
     resSize = seq.length();
+    resSize -= resSize%3;
+
     for(res = 0; res < resSize; res+=3)
     {
       String codon = seq.substring(res, res+3);
@@ -2546,16 +2583,18 @@ public void showTranslation_actionPerformed(ActionEvent e)
  */
 public boolean parseGroupsFile(String file)
 {
+    String line = null;
     try
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
       SequenceI seq = null;
-      String line, type, desc, token;
+      String type, desc, token;
 
       int index, start, end;
       StringTokenizer st;
       SequenceFeature sf;
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -2563,8 +2602,23 @@ public boolean parseGroupsFile(String file)
         if (st.countTokens() == 2)
         {
           type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          if (type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
+                ucs.findColour("A"));
+          }
           continue;
         }
 
@@ -2586,8 +2640,6 @@ public boolean parseGroupsFile(String file)
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
@@ -2598,7 +2650,7 @@ public boolean parseGroupsFile(String file)
             alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }
@@ -2606,11 +2658,14 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
-      System.out.println("Error parsing groups file: " + ex);
+      System.out.println(line);
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
       return false;
     }
 
     viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
     alignPanel.repaint();
     return true;
 }
@@ -2669,57 +2724,68 @@ public void drop(DropTargetDropEvent evt)
     {
       e.printStackTrace();
     }
-
     if (files != null)
     {
       try
       {
-        boolean isAnnotation = false;
 
         for (int i = 0; i < files.size(); i++)
         {
-          String file = files.get(i).toString();
-
-          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
-
-          if( !isAnnotation )
-          {
-            boolean isGroupsFile = parseGroupsFile(file);
-            if (!isGroupsFile)
-            {
-              String protocol = "File";
-              String format = jalview.io.IdentifyFile.Identify(file, protocol);
-              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
-
-              FastaFile ff = new FastaFile();
-              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-              c.setContents(new StringSelection(ff.print(sequences)), this);
-
-              this.paste(false);
-
-            }
-          }
+          loadJalviewDataFile(files.get(i).toString());
         }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
+  // This method will attempt to load a "dropped" file first by testing
+  // whether its and Annotation file, then features file. If both are
+  // false then the user may have dropped an alignment file onto this
+  // AlignFrame
+   public void loadJalviewDataFile(String file)
+  {
+    try{
+      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
+          alignment, file);
 
-        if(isAnnotation)
+      if (!isAnnotation)
+      {
+        boolean isGroupsFile = parseGroupsFile(file);
+        if (!isGroupsFile)
         {
-          int height = alignPanel.annotationPanel.adjustPanelHeight();
-          alignPanel.annotationScroller.setPreferredSize(
-              new Dimension(alignPanel.annotationScroller.getWidth(),
-                            height));
+          String protocol = "File";
+          String format = new IdentifyFile().Identify(file, protocol);
+          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,
+              format);
 
-          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              alignPanel.annotationSpaceFillerHolder.getWidth(),
-              height));
+          FastaFile ff = new FastaFile();
+          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+          c.setContents(new StringSelection(ff.print(sequences)), this);
 
-          alignPanel.addNotify();
+          this.paste(false);
         }
       }
-      catch (Exception ex)
+
+      if (isAnnotation)
       {
-        ex.printStackTrace();
+        int height = alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationScroller.setPreferredSize(
+            new Dimension(alignPanel.annotationScroller.getWidth(),
+                          height));
+
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            alignPanel.annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        alignPanel.addNotify();
       }
-    }
-}
 
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
 }