X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9566bb5731cf47301aecacb1e299a9f2c8b27436;hb=4c27b2c870cb1b4f858f7f4b52c4fe330a8e3b4c;hp=686ecbcd69938b117f0d6b80c95b2f78117d383b;hpb=d7b6fc2a38b90786ce62ea4e8a418e05b24e5352;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 686ecbc..9566bb5 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -36,8 +36,6 @@ public class AlignFrame extends GAlignFrame
     viewport = new AlignViewport(al,true,true,true,false);
     alignPanel = new AlignmentPanel(this, viewport);
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-    fontNameMenuItem.setText(viewport.getFont().getName());
-    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
 
     addInternalFrameListener(new InternalFrameAdapter()
    {
@@ -52,7 +50,6 @@ public class AlignFrame extends GAlignFrame
      }
    });
 
-   AlignmentUtil.fetchSequenceFeatures(al, alignPanel);
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
@@ -92,6 +89,23 @@ public class AlignFrame extends GAlignFrame
     htmlOutput = null;
   }
 
+  protected void createJPG_actionPerformed(ActionEvent e)
+  {
+
+    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
+    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
+
+
+    if(!viewport.getWrapAlignment())
+    {
+      height = viewport.alignment.getHeight() * viewport.charHeight;
+      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
+    }
+
+    alignPanel.makeJPG( width, height);
+  }
+
+
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
@@ -131,8 +145,8 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  ArrayList  historyList = new ArrayList();
-  ArrayList redoList = new ArrayList();
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
 
   void updateEditMenuBar()
   {
@@ -270,6 +284,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("Paste");
     paste(false);
   }
 
@@ -327,13 +342,24 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("Delete");
     if (viewport.getRubberbandGroup() == null)
       return;
 
      SequenceGroup sg = viewport.getRubberbandGroup();
      for (int i=0;i < sg.sequences.size(); i++)
-             viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));
+     {
+       SequenceI seq = sg.getSequenceAt(i);
+       int index = viewport.getAlignment().findIndex(seq);
+       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
 
+       if(seq.getSequence().length()<1)
+          viewport.getAlignment().deleteSequence(seq);
+      else
+          viewport.getAlignment().getSequences().setElementAt(seq, index);
+     }
+
+     viewport.setRubberbandGroup(null);
      viewport.alignment.deleteGroup(sg);
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
      if(viewport.getAlignment().getHeight()<1)
@@ -493,55 +519,15 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-
-  public void fontNameMenuItem_actionPerformed(ActionEvent e)
-  {
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
-
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font",
-                                "Font selection",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null,fonts
-                                ,fontNameMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-       fontNameMenuItem.setText(selection);
-       SetFont();
-     }
-
-  }
-
-  public void fontSizeMenuItem_actionPerformed(ActionEvent e)
-  {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font size",
-                                "Font size",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                                ,fontSizeMenuItem.getText()).toString();
-    if(selection!=null)
-     {
-       fontSizeMenuItem.setText(selection);
-       SetFont();
-     }
-  }
-
-  public void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  public void font_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font style",
-                                "Font style",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"plain", "bold", "italic"}
-                                ,fontStyleMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-      fontStyleMenuItem.setText(selection);
-      SetFont();
-    }
-
+    JOptionPane op = new JOptionPane();
+    JInternalFrame frame = op.createInternalFrame(this, "Change Font");
+    FontChooser fc = new FontChooser( alignPanel );
+    frame.setClosable(true);
+    frame.setContentPane(fc);
+    frame.setSize(480, 100);
+    frame.setVisible(true);
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
@@ -550,21 +536,6 @@ public class AlignFrame extends GAlignFrame
       alignPanel.RefreshPanels();
   }
 
-  void SetFont()
-  {
-      int style = java.awt.Font.PLAIN;
-      if(fontStyleMenuItem.getText().equals("bold"))
-        style = java.awt.Font.BOLD;
-      else if(fontStyleMenuItem.getText().equals("italic"))
-        style = java.awt.Font.ITALIC;
-
-      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
-                                           style,
-                                           Integer.parseInt(fontSizeMenuItem.getText())));
-      alignPanel.RefreshPanels();
-
-  }
-
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
@@ -594,6 +565,11 @@ public class AlignFrame extends GAlignFrame
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    {
+         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
+         ((Alignment)viewport.alignment).featuresAdded = true;
+    }
     alignPanel.RefreshPanels();
   }
 
@@ -956,22 +932,19 @@ if ( viewport.getConservationSelected() )
       return;
     }
 
-    JInternalFrame frame = new javax.swing.JInternalFrame();
     TreePanel tp=null;
    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
    {
      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         viewport.getStartRes(), viewport.getEndRes());
+                         0, viewport.alignment.getWidth());
    }
    else
    {
      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, viewport.getStartRes(),
-                         viewport.getEndRes());
+                         type, pwType,  0, viewport.alignment.getWidth());
    }
 
-   frame.setContentPane(tp);
-   Desktop.addInternalFrame(frame, title, 600, 500);
+   Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
 
@@ -1000,7 +973,7 @@ if ( viewport.getConservationSelected() )
       image = new Image[9];
       for(int i=0; i<9; i++)
       {
-        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
+        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
         if (url != null)
         {
           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);