selection removed, now SelectionGroup does same job as id select and residue select

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 96f4d4a..15f1a1f 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -55,8 +55,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    });\r
 \r
 \r
-   hscroll.setFocusable(false);\r
-   vscroll.setFocusable(false);\r
+  // hscroll.setFocusable(false);\r
+  // vscroll.setFocusable(false);\r
    setFocusable(true);\r
 \r
    addKeyListener(new KeyAdapter()\r
@@ -66,7 +66,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        switch(evt.getKeyCode())\r
        {\r
          case  27: // escape key\r
-           av.setRubberbandGroup(null);\r
+           av.setSelectionGroup(null);\r
            RefreshPanels();\r
            break;\r
          case KeyEvent.VK_X:\r
@@ -179,34 +179,83 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
   public void RefreshPanels()\r
   {\r
-    requestFocus();\r
-    invalidate();\r
-    seqPanel.seqCanvas.paintFlag = true;\r
-    idPanel.idCanvas.paintFlag = true;\r
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
+    javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+          {\r
+            public void run()\r
+            {\r
+\r
+              requestFocus();\r
+              invalidate();\r
+              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());\r
+              hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.\r
+                  getPreferredSize().width, 12));\r
+              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,\r
+                  av.charHeight / 2 + 12));\r
+              scalePanelHolder.setPreferredSize(new Dimension(500,\r
+                  av.charHeight / 2 + 12));\r
+              if (av.getWrapAlignment())\r
+              {\r
+                int max = av.alignment.getWidth() /\r
+                    (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\r
+\r
+                int h = (av.alignment.getHeight() + 2) * av.charHeight;\r
+                vextent = seqPanel.seqCanvas.getHeight() / h;\r
+                vscroll.setValues(0, vextent, 0, max);\r
+              }\r
+              else\r
+\r
+                setScrollValues(av.getStartRes(), av.getStartSeq());\r
+              av.getConsensus(true);\r
+              if (overviewPanel != null)\r
+                overviewPanel.updateOverviewImage();\r
+\r
+            }\r
+          });\r
+\r
+          validate();\r
+          repaint();\r
+  }\r
+  int hextent = 0;\r
+  int vextent = 0;\r
 \r
-    if(av.getWrapAlignment())\r
-    {\r
-      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
 \r
-      int h  = (av.alignment.getHeight() + 2)*av.charHeight;\r
-      vextent = seqPanel.seqCanvas.getHeight()/h;\r
-      vscroll.setValues(0,vextent,0,max);\r
+  // return value is true if the scroll is valid\r
+  public boolean scrollUp(boolean up)\r
+  {\r
+    if(up)\r
+    {\r
+      if(vscroll.getValue()<1)\r
+        return false;\r
+      vscroll.setValue(vscroll.getValue() - 1);\r
     }\r
     else\r
+    {\r
+     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
+       return false;\r
+      vscroll.setValue(vscroll.getValue() + 1);\r
+    }\r
 \r
-    setScrollValues(av.getStartRes(), av.getStartSeq());\r
-    av.getConsensus(true);\r
-    if(overviewPanel!=null)\r
-      overviewPanel.updateOverviewImage();\r
+    return true;\r
+  }\r
 \r
-    validate();\r
-    repaint();\r
+  public boolean scrollRight(boolean right)\r
+  {\r
+    if(right)\r
+   {\r
+     if(hscroll.getValue()<1)\r
+       return false;\r
+     hscroll.setValue(hscroll.getValue() - 1);\r
+   }\r
+   else\r
+   {\r
+    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())\r
+      return false;\r
+     hscroll.setValue(hscroll.getValue() + 1);\r
+   }\r
 \r
-  }\r
+   return true;\r
+ }\r
 \r
-  int hextent = 0;\r
-  int vextent = 0;\r
 \r
   public void setScrollValues(int x, int y)\r
   {\r
@@ -250,14 +299,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       if (av.getWrapAlignment())\r
       {\r
         av.setStartRes( vscroll.getValue() * av.getChunkWidth());\r
-        // System.out.println(vscroll.getValue()+" "+ av.getChunkWidth());\r
-      //  int resSpan = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
-     //   int h  = (av.alignment.getHeight() + 2)*av.charHeight;\r
-      //  vextent = seqPanel.seqCanvas.getHeight()/h;\r
-     //   vscroll.setValues(0,vextent,0,max);\r
-\r
-\r
-      // av.setStartSeq(  );\r
       }\r
       else\r
       {\r
@@ -270,7 +311,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(overviewPanel!=null)\r
       overviewPanel.setBoxPosition();\r
 \r
-    seqPanel.seqCanvas.paintFlag=true;\r
     repaint();\r
   }\r
 \r
@@ -324,7 +364,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     ////////////////\r
     //draw Scale\r
     pg.translate(idWidth,0);\r
-    scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
+    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
 \r
     pg.translate(-idWidth, 30);\r
     ////////////////\r
@@ -333,7 +373,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     Color currentTextColor=null;\r
     for(int i=startSeq; i<endSeq; i++)\r
     {\r
-      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
+      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)\r
       {\r
         currentColor = Color.gray;\r
         currentTextColor = Color.black;\r
@@ -440,6 +480,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
       javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(\r
           "LAST_DIRECTORY"));\r
+      chooser.setFileView(new jalview.io.JalviewFileView());\r
       chooser.setDialogTitle("Create JPG image from alignment");\r
       chooser.setToolTipText("Save");\r
 \r