X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=b0e5715cf10d701c533a8dff79fbc65c1c782312;hb=7c562dea24843c09b684eed45d0b71f7211166f0;hp=0c7f5d1b6db83a2f2ba71057cb3641186935916f;hpb=2794d58ed2b048de8cad254bea750f69d859240d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0c7f5d1..b0e5715 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -23,6 +23,7 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
+import jalview.commands.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
@@ -36,8 +37,8 @@ public class AlignFrame extends Frame implements ActionListener,
 {
   public AlignmentPanel alignPanel;
   public AlignViewport viewport;
-  int NEW_WINDOW_WIDTH = 700;
-  int NEW_WINDOW_HEIGHT = 500;
+  int DEFAULT_WIDTH = 700;
+  int DEFAULT_HEIGHT = 500;
 
   String jalviewServletURL;
 
@@ -91,13 +92,13 @@ public class AlignFrame extends Frame implements ActionListener,
         if (param != null)
         {
           int width = Integer.parseInt(param);
-          NEW_WINDOW_WIDTH = width;
+          DEFAULT_WIDTH = width;
         }
         param = applet.getParameter("windowHeight");
         if (param != null)
         {
           int height = Integer.parseInt(param);
-          NEW_WINDOW_HEIGHT = height;
+          DEFAULT_HEIGHT = height;
         }
       }
       catch (Exception ex)
@@ -132,8 +133,8 @@ public class AlignFrame extends Frame implements ActionListener,
    else
    {
      add(alignPanel, BorderLayout.CENTER);
-     jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
-                                      NEW_WINDOW_HEIGHT);
+     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+                                      DEFAULT_HEIGHT);
    }
    alignPanel.validate();
    alignPanel.repaint();
@@ -260,7 +261,10 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_SPACE:
         if(viewport.cursorMode)
         {
-          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
+          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown()
+              );
         }
         break;
 
@@ -268,7 +272,10 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_BACK_SPACE:
         if(viewport.cursorMode)
         {
-          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown()
+              );
         }
        else
         {
@@ -332,7 +339,7 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_H:
       {
         boolean toggleSeqs = !evt.isControlDown();
-        boolean toggleCols = !evt.isAltDown();
+        boolean toggleCols = !evt.isShiftDown();
         boolean hide = false;
         SequenceGroup sg = viewport.getSelectionGroup();
 
@@ -343,14 +350,18 @@ public class AlignFrame extends Frame implements ActionListener,
             hide = true;
             viewport.hideAllSelectedSeqs();
           }
-          else
+          else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
             viewport.showAllHiddenSeqs();
         }
 
         if(toggleCols)
         {
           if (viewport.colSel.getSelected().size() > 0)
+          {
             viewport.hideSelectedColumns();
+            if(!toggleSeqs)
+                   viewport.selectionGroup = sg;
+          }
           else if (!hide)
             viewport.showAllHiddenColumns();
         }
@@ -358,8 +369,23 @@ public class AlignFrame extends Frame implements ActionListener,
         alignPanel.repaint();
         break;
       }
-
-    }
+      case KeyEvent.VK_PAGE_UP:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(true);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     - viewport.endSeq + viewport.startSeq);
+        break;
+      case KeyEvent.VK_PAGE_DOWN:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(false);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     + viewport.endSeq - viewport.startSeq);
+        break;
+      }
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -579,6 +605,12 @@ public void itemStateChanged(ItemEvent evt)
       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
     }
 
+    if(viewport.applet.getParameter("jnetfile")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
+    }
+
     if(viewport.applet.getParameter("defaultColour")!=null)
     {
       url.append("&colour=" +
@@ -637,62 +669,21 @@ public void itemStateChanged(ItemEvent evt)
 
   void updateEditMenuBar()
   {
-    if (historyList.size() > 0)
-    {
-      undoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setLabel("Undo " + hi.getDescription());
-    }
-    else
-    {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setLabel("Undo");
-    }
-
-    if (redoList.size() > 0)
-    {
-      redoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setLabel("Redo " + hi.getDescription());
-    }
-    else
-    {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setLabel("Redo");
-    }
   }
 
-  public void addHistoryItem(HistoryItem hi)
-  {
-    historyList.push(hi);
-    updateEditMenuBar();
-  }
 
   protected void undoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
-                                  HistoryItem.HIDE));
-    restoreHistoryItem(hi);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) redoList.pop();
-    restoreHistoryItem(hi);
-    updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
   // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
+  void restoreHistoryItem(CommandI command)
   {
-    hi.restore();
-
-    updateEditMenuBar();
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -845,8 +836,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
+  //  addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+   //                                HistoryItem.PASTE));
     paste(false);
   }
 
@@ -909,8 +900,8 @@ public void itemStateChanged(ItemEvent evt)
         }
 
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                         NEW_WINDOW_HEIGHT);
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
+                                         DEFAULT_HEIGHT);
       }
       else
       {
@@ -933,8 +924,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
+    //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+    //                               HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -1036,154 +1027,18 @@ public void itemStateChanged(ItemEvent evt)
 
   public void remove2LeftMenuItem_actionPerformed()
   {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0, min);
-
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-      }
-
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveLeft(min))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
   }
 
   public void remove2RightMenuItem_actionPerformed()
   {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
-      }
-
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveRight(max))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
-
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    viewport.getAlignment().removeGaps();
-
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    SequenceI current;
-    int jSize;
-
-    Vector seqs=null;
-
-    int start=0, end = viewport.alignment.getWidth();
-
-    if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().getSequences(false) != null
-        && viewport.getSelectionGroup().getSize(false)>0)
-    {
-      seqs = viewport.getSelectionGroup().getSequences(true);
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes()+1;
-    }
-    else
-      seqs = viewport.alignment.getSequences();
-
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      current = (SequenceI) seqs.elementAt(i);
-      jSize = current.getLength();
-
-      // Removing a range is much quicker than removing gaps
-      // one by one for long sequences
-      int j = start;
-      int rangeStart=-1, rangeEnd=-1;
-
-      do
-      {
-        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          if(rangeStart==-1)
-           {
-             rangeStart = j;
-             rangeEnd = j+1;
-           }
-           else
-           {
-             rangeEnd++;
-           }
-           j++;
-        }
-        else
-        {
-          if(rangeStart>-1)
-          {
-            current.deleteChars(rangeStart, rangeEnd);
-            j-=rangeEnd-rangeStart;
-            jSize-=rangeEnd-rangeStart;
-            rangeStart = -1;
-            rangeEnd = -1;
-          }
-          else
-            j++;
-        }
-      }
-      while (j < end && j < jSize);
-      if(rangeStart>-1)
-      {
-       current.deleteChars(rangeStart, rangeEnd);
-      }
-    }
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void alignmentChanged()
@@ -1215,7 +1070,7 @@ public void itemStateChanged(ItemEvent evt)
                           viewport.alignment.getWidth());
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
       if (cs.conservationApplied())
       {
         Alignment al = (Alignment) viewport.alignment;
@@ -1455,7 +1310,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
 
     }
     viewport.setGlobalColourScheme(cs);
@@ -1590,8 +1445,8 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
@@ -1599,16 +1454,16 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortIDMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByID(viewport.getAlignment());
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+  //                                 HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     alignPanel.repaint();
 
@@ -1754,8 +1609,8 @@ public void itemStateChanged(ItemEvent evt)
     {
       public void actionPerformed(ActionEvent evt)
       {
-        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-                                       HistoryItem.SORT));
+      //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+      //                                 HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }