Applet has hidden regions

[jalview.git] / src / jalview / appletgui / PCAPanel.java

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 6465ee8..6559a17 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -36,6 +36,7 @@ public class PCAPanel
   RotatableCanvas rc;\r
   AlignViewport av;\r
   SequenceI [] seqs;\r
+  AlignmentView seqstrings;\r
 \r
 \r
   public PCAPanel(AlignViewport av)\r
@@ -57,23 +58,28 @@ public class PCAPanel
     }\r
 \r
     this.av = av;\r
-    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize(false) > 3)\r
+    seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+    if(av.getSelectionGroup()==null)\r
     {\r
-      seqs = new Sequence[av.getSelectionGroup().getSize(false)];\r
-      for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)\r
-      {\r
-        seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
-      }\r
+      seqs = av.alignment.getSequencesArray();\r
     }\r
     else\r
     {\r
-      seqs = new Sequence[av.getAlignment().getHeight()];\r
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+    }\r
+    SeqCigar sq[]=seqstrings.getSequences();\r
+    int length = sq[0].getWidth();\r
+\r
+    for (int i = 0; i < seqs.length; i++)\r
+    {\r
+      if (sq[i].getWidth() != length)\r
       {\r
-        seqs[i] = av.getAlignment().getSequenceAt(i);\r
+        System.out.println("Sequences must be equal length for PCA analysis");\r
+        return;\r
       }\r
     }\r
 \r
+\r
     rc = new RotatableCanvas(av);\r
     add(rc, BorderLayout.CENTER);\r
 \r
@@ -90,7 +96,7 @@ public class PCAPanel
    */\r
   public void run()\r
   {\r
-              pca = null;//new PCA(seqs);\r
+              pca = new PCA(seqstrings.getSequenceStrings(' '));\r
               pca.run();\r
 \r
               // Now find the component coordinates\r
@@ -158,7 +164,10 @@ public class PCAPanel
 \r
   public void actionPerformed(ActionEvent evt)\r
   {\r
-    values_actionPerformed();\r
+    if(evt.getSource()==inputData)\r
+      showOriginalData();\r
+    else\r
+      values_actionPerformed();\r
   }\r
 \r
   public void itemStateChanged(ItemEvent evt)\r
@@ -198,6 +207,28 @@ public class PCAPanel
       cap.setText(pca.getDetails());\r
   }\r
 \r
+  void showOriginalData()\r
+  {\r
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+    // or create a selection box around columns in alignment view\r
+    // test Alignment(SeqCigar[])\r
+    Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
+        getGapCharacter());\r
+\r
+\r
+    if (alAndColsel != null && alAndColsel[0]!=null)\r
+     {\r
+       Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+       AlignFrame af = new AlignFrame(al,\r
+             av.applet,\r
+             "Original Data for PCA",\r
+             false);\r
+\r
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );\r
+     }\r
+  }\r
+\r
   public void labels_itemStateChanged(ItemEvent itemEvent)\r
   {\r
     rc.showLabels( labels.getState() );\r
@@ -216,6 +247,7 @@ public class PCAPanel
   Menu menu2 = new Menu();\r
   protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
   MenuItem values = new MenuItem();\r
+  MenuItem inputData = new MenuItem();\r
 \r
   private void jbInit()\r
       throws Exception\r
@@ -242,6 +274,7 @@ public class PCAPanel
     labels.addItemListener(this);\r
     values.setLabel("Output Values...");\r
     values.addActionListener(this);\r
+    inputData.setLabel("Input Data...");\r
     this.add(jPanel2, BorderLayout.SOUTH);\r
     jPanel2.add(jLabel1, null);\r
     jPanel2.add(xCombobox, null);\r
@@ -253,6 +286,8 @@ public class PCAPanel
     menuBar1.add(menu2);\r
     menu2.add(labels);\r
     menu1.add(values);\r
+    menu1.add(inputData);\r
+    inputData.addActionListener(this);\r
   }\r
 \r
 }\r