X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=784df09ff0bd05a2b172718b01e0be9e3438f91f;hb=3af1fc9be996fd7a943a72e137b3ac6b49862770;hp=a4f5e4d917635f73fff1555873fb1a0a2049ac1d;hpb=be545261cf6e7225da6f3ac1306b1b2609fd0e70;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a4f5e4d..784df09 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -54,9 +54,6 @@ public class AlignFrame
   AlignmentPanel alignPanel;
   AlignViewport viewport;
 
-  Vector viewports = new Vector();
-  Vector alignPanels = new Vector();
-
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
   Stack historyList = new Stack();
@@ -72,7 +69,6 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
-    viewports.add(viewport);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
@@ -88,7 +84,6 @@ public class AlignFrame
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanels.add(alignPanel);
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
@@ -195,6 +190,11 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");
   }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+  }
+
 
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
@@ -263,7 +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;
@@ -360,6 +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!
    *
@@ -685,6 +706,11 @@ 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!!<<<
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
         if (title.startsWith("Copied sequences"))
         {
           newtitle = title;
@@ -776,7 +802,7 @@ public class AlignFrame
 
     //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)
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
       for (int i = 0; i < sg.sequences.size(); i++)
       {
@@ -797,7 +823,7 @@ public class AlignFrame
           j++;
         }while(j<=sg.getEndRes());
       }
-    }
+    }*/
 
 
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
@@ -887,6 +913,11 @@ 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);
@@ -1109,7 +1140,10 @@ 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();
@@ -1171,8 +1205,11 @@ 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();
   }
 
   /**
@@ -1903,6 +1940,13 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1952,7 +1996,7 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 3))
@@ -2004,7 +2048,6 @@ public class AlignFrame
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2313,6 +2356,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2324,7 +2368,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2341,7 +2385,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }
 
@@ -2465,42 +2509,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations
       = viewport.alignment.getAlignmentAnnotation();
   int a, aSize;
-  for (int i = 0; i < annotations.length; i++)
+  if(annotations!=null)
   {
-
-    if (annotations[i].label.equals("Quality") ||
-        annotations[i].label.equals("Conservation") ||
-        annotations[i].label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
     {
-      continue;
-    }
-
+      if (annotations[i].label.equals("Quality") ||
+          annotations[i].label.equals("Conservation") ||
+          annotations[i].label.equals("Consensus"))
+      {
+        continue;
+      }
 
-    aSize = viewport.alignment.getWidth()/3;
-    jalview.datamodel.Annotation [] anots =
-        new jalview.datamodel.Annotation[aSize];
+      aSize = viewport.alignment.getWidth() / 3;
+      jalview.datamodel.Annotation[] anots =
+          new jalview.datamodel.Annotation[aSize];
 
-    for(a=0; a<viewport.alignment.getWidth(); a++)
-    {
-     if( annotations[i].annotations[a]==null
-      || annotations[i].annotations[a]==null)
-       continue;
+      for (a = 0; a < viewport.alignment.getWidth(); a++)
+      {
+        if (annotations[i].annotations[a] == null
+            || annotations[i].annotations[a] == null)
+          continue;
 
-      anots[a/3] = new Annotation(
-     annotations[i].annotations[a].displayCharacter,
-     annotations[i].annotations[a].description,
-     annotations[i].annotations[a].secondaryStructure,
-     annotations[i].annotations[a].value,
-     annotations[i].annotations[a].colour);
-    }
+        anots[a / 3] = new Annotation(
+            annotations[i].annotations[a].displayCharacter,
+            annotations[i].annotations[a].description,
+            annotations[i].annotations[a].secondaryStructure,
+            annotations[i].annotations[a].value,
+            annotations[i].annotations[a].colour);
+      }
 
-    jalview.datamodel.AlignmentAnnotation aa
+      jalview.datamodel.AlignmentAnnotation aa
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-       annotations[i].description, anots );
-     al.addAnnotation(aa);
+          annotations[i].description, anots);
+      al.addAnnotation(aa);
+    }
   }
 
-
     AlignFrame af = new AlignFrame(al);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              NEW_WINDOW_WIDTH,
@@ -2608,8 +2652,7 @@ public boolean parseGroupsFile(String file)
             alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end);
-          sf.setFeatureGroup(featureGroup);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }
@@ -2683,57 +2726,68 @@ 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 = new 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();
+      }
+    }
+}
 
-        if(isAnnotation)
+  // 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)
+      {
+        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();
+    }
+  }
 }