X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b714aea53cabf9b96dea336328ca497d1ca28d14;hb=49057b644ae4dc904a3245b695ba86678ac01ede;hp=de2d3d150fa821af6b2dd2bd2779a879f15a31c3;hpb=ce23b7810e0a9fea03e3f46a14319e1012d4eabf;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index de2d3d1..b714aea 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!
    *
@@ -698,7 +691,7 @@ 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)
@@ -760,8 +753,16 @@ public class AlignFrame
             viewport.alignment.getDataset().addSequence(ds);
           }
           else
+          {
             newseq.setDatasetSequence(sequences[i].getDatasetSequence());
-
+            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
+            {
+              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
+              {
+                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
+              }
+            }
+          }
         }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
@@ -802,24 +803,50 @@ 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);
@@ -898,7 +925,7 @@ public class AlignFrame
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.annotationPanel.activeRes = null;
+    alignPanel.idPanel.idCanvas.searchResults = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -1192,8 +1219,8 @@ 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);
   }
 
   /**
@@ -1320,25 +1347,37 @@ 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();
   }
 
   /**
@@ -2416,10 +2455,7 @@ public class AlignFrame
     }
   }*/
 
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
+
 
 
 
@@ -2436,6 +2472,8 @@ 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);
@@ -2547,6 +2585,7 @@ public boolean parseGroupsFile(String file)
       StringTokenizer st;
       SequenceFeature sf;
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -2554,8 +2593,23 @@ 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;
         }
 
@@ -2577,8 +2631,6 @@ 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();
 
@@ -2590,6 +2642,7 @@ public boolean parseGroupsFile(String file)
           }
 
           sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }
@@ -2597,11 +2650,13 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
       System.out.println("Error parsing groups file: " + ex);
       return false;
     }
 
     viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
     alignPanel.repaint();
     return true;
 }
@@ -2679,7 +2734,7 @@ public void drop(DropTargetDropEvent evt)
             if (!isGroupsFile)
             {
               String protocol = "File";
-              String format = jalview.io.IdentifyFile.Identify(file, protocol);
+              String format = new IdentifyFile().Identify(file, protocol);
               SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
 
               FastaFile ff = new FastaFile();