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 1201278..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
@@ -124,7 +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
@@ -140,7 +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
@@ -163,7 +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
@@ -175,14 +178,16 @@ public class Finder extends Panel implements ActionListener
 \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
@@ -297,7 +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
@@ -329,10 +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