From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 8 Jul 2015 12:19:14 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
X-Git-Tag: Jalview_2_9~12^2~3
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=f0abe70b5a54b6a9730aa5f4e2bf2bd697508757;hp=1ba05544b34253204ef6410017a179c31fe5e23d

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
---

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index dcb2a7d..99bcff4 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -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;
 
@@ -260,13 +258,6 @@ 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 +273,8 @@ 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 +285,7 @@ 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 +298,7 @@ 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())
         {
@@ -723,4 +715,42 @@ 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;
+  }
 }
diff --git a/test/jalview/gui/AppVarnaTest.java b/test/jalview/gui/AppVarnaTest.java
new file mode 100644
index 0000000..94a3300
--- /dev/null
+++ b/test/jalview/gui/AppVarnaTest.java
@@ -0,0 +1,24 @@
+package jalview.gui;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+
+import org.testng.annotations.Test;
+
+public class AppVarnaTest
+{
+  @Test
+  public void testReplaceOddGaps()
+  {
+    String struct = "{(<]}>)";
+    String replaced = AppVarna.replaceOddGaps(struct);
+    assertEquals(struct, replaced);
+    assertSame(struct, replaced);
+    assertEquals("..{.([.<.].}.>)",
+            AppVarna.replaceOddGaps("..{ ([*<-]?} >)"));
+    assertEquals("....", AppVarna.replaceOddGaps("cgta"));
+    assertEquals("", AppVarna.replaceOddGaps(""));
+    assertNull(AppVarna.replaceOddGaps(null));
+  }
+}