Merge branch 'Release_2_9_0b1_Branch'

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index dcb2a7d..038de29 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -43,8 +43,6 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JSplitPane;
@@ -66,8 +64,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
         SecondaryStructureListener, InterfaceVARNASelectionListener,
         VamsasSource
 {
-  private static final Pattern PAIRS_PATTERN = Pattern
-          .compile("[^([{<>}])]");
+  private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+      '}', '<', '>' };
 
   private AppVarnaBinding vab;
 
@@ -183,8 +181,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     String theTitle = sname
             + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
     theTitle = MessageManager.formatMessage("label.varna_params",
-            new String[]
-            { theTitle });
+            new String[] { theTitle });
     setTitle(theTitle);
 
     String gappedTitle = sname + " (with gaps)";
@@ -197,7 +194,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(0);
   }
 
-
   /**
    * Constructor that links the viewer to a parent panel (but has no structures
    * yet - use addModel to add them)
@@ -260,13 +256,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     showPanel(true);
   }
 
-  public String replaceOddGaps(String oldStr)
-  {
-    Matcher matcher = PAIRS_PATTERN.matcher(oldStr);
-    String newStr = matcher.replaceAll(".");
-    return newStr;
-  }
-
   /**
    * Constructs a new RNA model from the given one, without gaps. Also
    * calculates and saves a 'shift list'
@@ -282,7 +271,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     RNA rnaTrim = new RNA(name);
     try
     {
-      rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
+      String structDBN = rna.getStructDBN(true);
+      rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN));
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -293,7 +283,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
 
     String seq = rnaTrim.getSeq();
     StringBuilder struc = new StringBuilder(256);
-    struc.append(rnaTrim.getStructDBN());
+    struc.append(rnaTrim.getStructDBN(true));
     int ofstart = -1;
     int sleng = seq.length();
 
@@ -306,7 +296,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
           ofstart = i;
         }
         /*
-         * mark base or base pair in the structure with *
+         * mark base or base & pair in the structure with *
          */
         if (!rnaTrim.findPair(i).isEmpty())
         {
@@ -685,7 +675,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(selectedIndex);
   }
 
-
   /**
    * Add a model with associated Varna session file
    * 
@@ -723,4 +712,41 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
       return null;
     }
   }
+
+  /**
+   * Replace everything except RNA secondary structure characters with a period
+   * 
+   * @param s
+   * @return
+   */
+  public static String replaceOddGaps(String s)
+  {
+    if (s == null)
+    {
+      return null;
+    }
+
+    // this is measured to be 10 times faster than a regex replace
+    boolean changed = false;
+    byte[] bytes = s.getBytes();
+    for (int i = 0; i < bytes.length; i++)
+    {
+      boolean ok = false;
+      // todo check for ((b >= 'a' && b <= 'z') || (b >= 'A' && b <= 'Z')) if
+      // wanted also
+      for (int j = 0; !ok && (j < PAIRS.length); j++)
+      {
+        if (bytes[i] == PAIRS[j])
+        {
+          ok = true;
+        }
+      }
+      if (!ok)
+      {
+        bytes[i] = '.';
+        changed = true;
+      }
+    }
+    return changed ? new String(bytes) : s;
+  }
 }