Highlight sequences to be deleted before deleting, and apply button exists

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 504338a..2732612 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -23,95 +23,232 @@ import java.util.*;
 \r
 import java.awt.event.*;\r
 \r
+import java.awt.*;\r
+\r
 import jalview.datamodel.*;\r
+import jalview.appletgui.PaintRefresher;\r
 \r
-public class RedundancyPanel extends SliderPanel\r
+public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener\r
 {\r
   AlignmentPanel ap;\r
 \r
+  Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+  Vector originalSequences;\r
+  Hashtable originalColours;\r
   SequenceI[] oldAlignment;\r
+  float [] redundancy;\r
+  Frame frame;\r
 \r
   public RedundancyPanel(AlignmentPanel ap)\r
   {\r
     super(ap, 0, false, null);\r
 \r
     this.ap = ap;\r
+    undoButton.setVisible(true);\r
+    applyButton.setVisible(true);\r
+    allGroupsCheck.setVisible(false);\r
 \r
     label.setText("Enter the redundancy threshold");\r
+    valueField.setText("100");\r
+\r
+    slider.setVisibleAmount(1);\r
+    slider.setMinimum(40);\r
+    slider.setMaximum(100+slider.getVisibleAmount());\r
+    slider.setValue(100);\r
 \r
     slider.addAdjustmentListener(new AdjustmentListener()\r
     {\r
       public void adjustmentValueChanged(AdjustmentEvent evt)\r
       {\r
         valueField.setText(slider.getValue() + "");\r
+        sliderValueChanged();\r
       }\r
     });\r
 \r
-    slider.setMinimum(0);\r
-    slider.setMaximum(100);\r
-    slider.setValue(100);\r
+    frame = new Frame();\r
+    frame.add(this);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
+                                     400, 100);\r
 \r
-  }\r
+    frame.addWindowListener(this);\r
 \r
-  public void applyButton_actionPerformed()\r
+    Thread worker = new Thread(this);\r
+    worker.start();\r
+  }\r
+  /**\r
+   * This is a copy of remove redundancy in jalivew.datamodel.Alignment\r
+   * except we dont want to remove redundancy, just calculate once\r
+   * so we can use the slider to dynamically hide redundant sequences\r
+   *\r
+   * @param threshold DOCUMENT ME!\r
+   * @param sel DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public void run()\r
   {\r
-    float threshold = slider.getValue();\r
-    Vector del;\r
+      label.setText("Calculating....");\r
 \r
-    oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
-    for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
-    {\r
-      oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
-                                     ap.av.alignment.getSequenceAt(i).\r
-                                     getSequence());\r
-    }\r
+      slider.setVisible(false);\r
+      applyButton.setEnabled(false);\r
+      valueField.setVisible(false);\r
 \r
-    undoButton.setEnabled(true);\r
+      validate();\r
 \r
-    SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if (sg != null && sg.getSize() > 1)\r
-    {\r
+      Vector sel = new Vector();\r
+      SequenceGroup sg = ap.av.getSelectionGroup();\r
+      int height;\r
+      originalSequences = new Vector();\r
+      originalColours = new Hashtable();\r
 \r
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
-      for (int i = 0; i < del.size(); i++)\r
+      if ( (sg != null) && (sg.getSize() >= 1))\r
       {\r
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
+         height = sg.getSize();\r
+        for (int i = 0; i < sg.getSize(); i++)\r
         {\r
-          sg.deleteSequence( (SequenceI) del.elementAt(i), true);\r
+          sel.addElement(sg.getSequenceAt(i));\r
+        }\r
+      }\r
+      else\r
+      {\r
+        height = ap.av.alignment.getHeight();\r
+        for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+        {\r
+          sel.addElement(ap.av.alignment.getSequenceAt(i));\r
         }\r
       }\r
 \r
-    }\r
-    else\r
-    {\r
-      Vector s = new Vector();\r
-      int i = 0;\r
-      while (i < ap.av.alignment.getHeight())\r
+      redundancy = new float[height];\r
+      for (int i = 0; i < height; i++)\r
       {\r
-        s.addElement(ap.av.alignment.getSequenceAt(i));\r
-        i++;\r
+        redundancy[i] = 0f;\r
       }\r
-      del = ap.av.alignment.removeRedundancy(threshold, s);\r
-      for (int j = 0; j < del.size(); j++)\r
+\r
+\r
+     // long start = System.currentTimeMillis();\r
+\r
+      float pid;\r
+      SequenceI seqi, seqj;\r
+      for (int i = 0; i < sel.size(); i++)\r
       {\r
-        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))\r
-        {\r
-          sg.deleteSequence( (SequenceI) del.elementAt(j), true);\r
-        }\r
+          originalSequences.addElement(sel.elementAt(i));\r
+          originalColours.put(sel.elementAt(i),\r
+                             ((SequenceI) sel.elementAt(i)).getColor());\r
+\r
+          for (int j = 0; j < i; j++)\r
+          {\r
+            if(i==j)\r
+              continue;\r
+\r
+            seqi = (SequenceI) sel.elementAt(i);\r
+            seqj = (SequenceI) sel.elementAt(j);\r
 \r
+            if (sg != null)\r
+            {\r
+              pid = jalview.util.Comparison.PID(seqi,\r
+                                                seqj,\r
+                                                sg.getStartRes(), sg.getEndRes());\r
+            }\r
+            else\r
+              pid = jalview.util.Comparison.PID( seqi,  seqj );\r
+\r
+\r
+            if(seqj.getLength() < seqi.getLength())\r
+              redundancy[j] = Math.max(pid, redundancy[j]);\r
+            else\r
+              redundancy[i] = Math.max(pid, redundancy[i]);\r
+\r
+          }\r
       }\r
+\r
+\r
+      label.setText("Enter the redundancy threshold");\r
+      slider.setVisible(true);\r
+      applyButton.setEnabled(true);\r
+      valueField.setVisible(true);\r
+\r
+      validate();\r
+     // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
+  }\r
+\r
+  void sliderValueChanged()\r
+  {\r
+    if(redundancy==null)\r
+      return;\r
+\r
+    float value = slider.getValue();\r
+\r
+    for(int i=0; i<redundancy.length; i++)\r
+    {\r
+      if (value > redundancy[i])\r
+         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
+      else\r
+         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+    }\r
+\r
+    PaintRefresher.Refresh(null,ap.av.alignment);\r
+\r
     }\r
+  public void applyButton_actionPerformed()\r
+  {\r
+    historyList.push(new HistoryItem("Remove redundancy",\r
+                        ap.av.alignment, HistoryItem.HIDE));\r
+\r
+            if ((historyList.size() == 1) ||\r
+                    !ap.alignFrame.historyList.contains(historyList.firstElement()))\r
+            {\r
+                ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());\r
+                ap.alignFrame.updateEditMenuBar();\r
+            }\r
+\r
+            Vector del = new Vector();\r
+\r
+            undoButton.setEnabled(true);\r
+\r
+            float value = slider.getValue();\r
+            SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+            for (int i = 0; i < redundancy.length; i++)\r
+            {\r
+              if (value <= redundancy[i])\r
+              {\r
+                SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+                ap.av.alignment.deleteSequence(seq);\r
+                del.addElement(seq);\r
+                if (sg != null)\r
+                {\r
+                  sg.deleteSequence(seq, false);\r
+                }\r
+              }\r
+            }\r
 \r
-    ap.repaint();\r
+\r
+            // This has to be done before the restoreHistoryItem method of alignFrame will\r
+            // actually restore these sequences.\r
+            if (del.size() > 0)\r
+            {\r
+                for (int i = 0, j = del.size(); i < j; i++)\r
+                {\r
+                    SequenceI sq = (SequenceI) del.elementAt(i);\r
+                    sq.deleteChars(0, sq.getLength());\r
+                }\r
+            }\r
+\r
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+        ap.alignFrame.updateEditMenuBar();\r
 \r
   }\r
 \r
   public void undoButton_actionPerformed()\r
   {\r
-    undoButton.setEnabled(false);\r
-    ap.av.setAlignment(new Alignment(oldAlignment));\r
-    oldAlignment = null;\r
-    ap.repaint();\r
+    HistoryItem hi = (HistoryItem) historyList.pop();\r
+    ap.alignFrame.restoreHistoryItem(hi);\r
+\r
+    if (historyList.size() == 0)\r
+    {\r
+      undoButton.setEnabled(false);\r
+    }\r
+    ap.alignFrame.updateEditMenuBar();\r
   }\r
 \r
   public void valueField_actionPerformed(ActionEvent e)\r
@@ -126,4 +263,31 @@ public class RedundancyPanel extends SliderPanel
       valueField.setText(slider.getValue() + "");\r
     }\r
   }\r
+\r
+\r
+  public void windowOpened(WindowEvent evt)\r
+  {}\r
+\r
+  public void windowClosing(WindowEvent evt)\r
+  {\r
+    for(int i=0; i<originalSequences.size(); i++)\r
+    {\r
+      SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
+      seq.setColor( (java.awt.Color)originalColours.get(seq));\r
+    }\r
+\r
+    PaintRefresher.Refresh(ap.av.alignment);\r
+  }\r
+\r
+  public void windowClosed(WindowEvent evt)\r
+  {}\r
+\r
+  public void windowActivated(WindowEvent evt)\r
+  {}\r
+  public void windowDeactivated(WindowEvent evt)\r
+  {}\r
+  public void windowIconified(WindowEvent evt)\r
+  {}\r
+  public void windowDeiconified(WindowEvent evt)\r
+  {}\r
 }\r