Implemented CIGAR representation of an Alignment view for passing to

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index fb8c280..47b756d 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -25,6 +25,7 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 import jalview.datamodel.*;\r
+import java.awt.Rectangle;\r
 \r
 public class Finder extends Panel implements ActionListener\r
 {\r
@@ -84,20 +85,37 @@ public class Finder extends Panel implements ActionListener
   public void createNewGroup_actionPerformed()\r
   {\r
 \r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\r
+    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);\r
+    dialog.add(cap);\r
+\r
+    cap.setText(textfield.getText());\r
+\r
+    dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,\r
+                      frame.getLocation().y+20,300,100);\r
+    dialog.show();\r
+\r
+\r
+    String featureName = cap.getText().trim();\r
+    if(featureName.length()<1)\r
+      return;\r
+\r
+\r
     for (int i = 0; i < searchResults.getSize(); i ++ )\r
     {\r
         SequenceI seq = searchResults.getResultSequence(i);\r
 \r
-        SequenceFeature sf = new SequenceFeature(textfield.getText(),\r
-            "Search Results", null,\r
+        SequenceFeature sf = new SequenceFeature(featureName,\r
+            null, null,\r
             searchResults.getResultStart(i),\r
-           searchResults.getResultEnd(i));\r
+           searchResults.getResultEnd(i), "Search Results");\r
 \r
         ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
-            textfield.getText(), new Color(60,160,115));\r
+            featureName, new Color(60,160,115));\r
         seq.addSequenceFeature(sf);\r
     }\r
 \r
+    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
     ap.alignFrame.sequenceFeatures.setState(true);\r
     av.showSequenceFeatures(true);\r
     ap.highlightSearchResults(null);\r
@@ -107,7 +125,9 @@ public class Finder extends Panel implements ActionListener
   {\r
     createNewGroup.setEnabled(false);\r
 \r
-    String searchString = textfield.getText().toUpperCase();\r
+    String searchString = textfield.getText();\r
+    if(!caseSensitive.getState())\r
+      searchString = searchString.toUpperCase();\r
 \r
     com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
 \r
@@ -123,7 +143,7 @@ public class Finder extends Panel implements ActionListener
       int res = Integer.parseInt(searchString);\r
       found = true;\r
 \r
-      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
       {\r
         seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
       }\r
@@ -146,7 +166,7 @@ public class Finder extends Panel implements ActionListener
     SequenceGroup selection = av.getSelectionGroup();\r
     if (selection != null)\r
     {\r
-      if (selection.getSize() < 1 ||\r
+      if (selection.getSize(false) < 1 ||\r
           (selection.getEndRes() - selection.getStartRes() < 2))\r
       {\r
         selection = null;\r
@@ -155,16 +175,19 @@ public class Finder extends Panel implements ActionListener
 \r
     while (!found && seqIndex < end)\r
     {\r
+\r
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
-      if (selection != null && !selection.sequences.contains(seq))\r
+      if (selection != null && !selection.getSequences(false).contains(seq))\r
       {\r
         seqIndex++;\r
         resIndex = 0;\r
         continue;\r
       }\r
 \r
-      item = seq.getSequence().toUpperCase();\r
+      item = seq.getSequence();\r
+      if(!caseSensitive.getState())\r
+        item = item.toUpperCase();\r
 \r
       if (selection != null && selection.getEndRes() < av.alignment.getWidth())\r
       {\r
@@ -172,7 +195,7 @@ public class Finder extends Panel implements ActionListener
       }\r
 \r
       ///Shall we ignore gaps????\r
-      StringBuffer noGaps = new StringBuffer();\r
+      StringBuffer noGapsSB = new StringBuffer();\r
       int insertCount = 0;\r
       Vector spaces = new Vector();\r
 \r
@@ -181,7 +204,7 @@ public class Finder extends Panel implements ActionListener
 \r
         if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
         {\r
-          noGaps.append(item.charAt(j));\r
+          noGapsSB.append(item.charAt(j));\r
           spaces.addElement(new Integer(insertCount));\r
         }\r
         else\r
@@ -190,10 +213,12 @@ public class Finder extends Panel implements ActionListener
         }\r
       }\r
 \r
+      String noGaps = noGapsSB.toString();\r
+\r
       for (int r = resIndex; r < noGaps.length(); r++)\r
       {\r
 \r
-        if (regex.searchFrom(noGaps.toString(), r))\r
+        if (regex.searchFrom(noGaps, r))\r
         {\r
           resIndex = regex.matchedFrom();\r
           if (selection != null &&\r
@@ -264,8 +289,8 @@ public class Finder extends Panel implements ActionListener
 \r
     if (findAll)\r
     {\r
-      String message = (searchResults.getSize()) + " matches found.";\r
-      System.out.println(message);\r
+      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";\r
+      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);\r
     }\r
 \r
   }\r
@@ -277,7 +302,7 @@ public class Finder extends Panel implements ActionListener
   Panel jPanel1 = new Panel();\r
   GridLayout gridLayout1 = new GridLayout();\r
   protected Button createNewGroup = new Button();\r
-\r
+  Checkbox caseSensitive = new Checkbox();\r
 \r
   private void jbInit() throws Exception {\r
       jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
@@ -309,10 +334,13 @@ public class Finder extends Panel implements ActionListener
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
       createNewGroup.setLabel("New Feature");\r
       createNewGroup.addActionListener(this);\r
-      jPanel1.add(findNext, null);\r
+    caseSensitive.setLabel("Match Case");\r
+    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));\r
+    jPanel1.add(findNext, null);\r
       jPanel1.add(findAll, null);\r
       jPanel1.add(createNewGroup, null);\r
-      this.add(textfield, null);\r
+    this.add(caseSensitive);\r
+    this.add(textfield, null);\r
       this.add(jLabel1, null);\r
       this.add(jPanel1, null);\r
   }\r