isGap method added to utils

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index f99661e..eed6d0a 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -119,17 +119,19 @@ public class Conservation {
     }\r
   }\r
 \r
-  public int countGaps(int j) {\r
+  public int countGaps(int j)\r
+  {\r
     int count = 0;\r
 \r
-    for (int i = 0; i < sequences.size();i++) {\r
+    for (int i = 0; i < sequences.size();i++)\r
+    {\r
       if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
       {  count++; continue;}\r
 \r
-      String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
-      if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\r
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
+      if (jalview.util.Comparison.isGap((c)))\r
         count++;\r
-      }\r
+\r
     }\r
     return count;\r
   }\r

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc5d760..d35cbe8 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -144,19 +144,18 @@ public class Sequence implements SequenceI
 \r
     while (i< sequence.length() && j <= end && j <= pos) {\r
 \r
-      String s = sequence.substring(i,i+1);\r
+      char c = sequence.charAt(i);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         j++;\r
-      }\r
+\r
       i++;\r
     }\r
-    if (j == end && j < pos) {\r
+    if (j == end && j < pos)\r
       return end+1;\r
-    } else {\r
-\r
+    else\r
       return i;\r
-    }\r
+\r
   }\r
 \r
   public int findPosition(int i) {\r
@@ -164,12 +163,13 @@ public class Sequence implements SequenceI
     int j   = 0;\r
     int pos = start;\r
 \r
-    while (j < i) {\r
-      String s = sequence.substring(j,j+1);\r
+    while (j < i)\r
+    {\r
+      char c = sequence.charAt(j);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         pos++;\r
-      }\r
+\r
       j++;\r
     }\r
     return pos;\r

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2512978..cba91df 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -161,12 +161,12 @@ public class SequenceFeature {
       }\r
 \r
       for (int i = fstart; i <= fend; i++) {\r
-        String s = sequence.sequence.substring(i,i+1);\r
-        if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+        char c = sequence.sequence.charAt(i);\r
+        if (!jalview.util.Comparison.isGap((c)))\r
           g.fillRect(x1+(i-fstart)*width,y1,width,height);\r
-        } else {\r
+        else\r
           g.drawString("-",x1+(i-fstart)*width,y1+height);\r
-        }\r
+\r
       }\r
 \r
     }\r

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 72fb1d1..d8e599b 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -16,27 +16,22 @@ public class Comparison {
      int ilen = end-start+1;\r
      int jlen = end-start+1;\r
 \r
-     if ( si.substring(start + ilen).equals("-") ||\r
-          si.substring(start + ilen).equals(".") ||\r
-          si.substring(start + ilen).equals(" ")) {\r
-\r
+     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )\r
+      {\r
        ilen--;\r
 \r
-       while (si.substring(start + ilen,start + ilen+1).equals("-")  ||\r
-              si.substring(start + ilen,start + ilen+1).equals(".")  ||\r
-              si.substring(start + ilen,start + ilen+1).equals(" ")) {\r
+       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))\r
+       {\r
          ilen--;\r
        }\r
      }\r
 \r
-     if ( sj.substring(start + jlen).equals("-")  ||\r
-          sj.substring(start + jlen).equals(".")  ||\r
-          sj.substring(start + jlen).equals(" ")) {\r
+     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )\r
+     {\r
        jlen--;\r
 \r
-       while (sj.substring(start + jlen,start + jlen+1).equals("-")  ||\r
-              sj.substring(start + jlen,start + jlen+1).equals(".")  ||\r
-              sj.substring(start + jlen,start + jlen+1).equals(" ")) {\r
+       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))\r
+       {\r
          jlen--;\r
        }\r
      }\r
@@ -68,47 +63,47 @@ public class Comparison {
   }\r
 \r
   /**    */\r
-  public static float PID(Sequence s1 , Sequence s2) {\r
-    int res = 0;\r
+  public static float PID(Sequence s1 , Sequence s2)\r
+  {\r
     int len;\r
 \r
-    if (s1.getSequence().length() > s2.getSequence().length()) {\r
+    if (s1.getSequence().length() > s2.getSequence().length())\r
       len = s1.getSequence().length();\r
-    } else {\r
+    else\r
       len = s2.getSequence().length();\r
-    }\r
+\r
 \r
     int bad = 0;\r
 \r
-    for (int i = 0; i < len; i++) {\r
-      String str1 = "";\r
-      String str2 = "";\r
+    for (int i = 0; i < len; i++)\r
+    {\r
+      char chr1;\r
+      char chr2;\r
 \r
-      if (i < s1.getSequence().length()) {\r
-        str1 = s1.getSequence().substring(i,i+1);\r
-      } else {\r
-        str1 = ".";\r
-      }\r
+      if (i < s1.getSequence().length())\r
+        chr1 = s1.getSequence().charAt(i);\r
+      else\r
+        chr1 = '.';\r
 \r
-      if (i < s2.getSequence().length()) {\r
-        str2 = s2.getSequence().substring(i,i+1);\r
-      } else {\r
-        str2 = ".";\r
-      }\r
 \r
-      if (!(str1.equals(".") ||\r
-            str1.equals("-") ||\r
-            str1.equals(" "))   &&\r
-          !(str2.equals(".") ||\r
-            str2.equals("-") ||\r
-            str2.equals(" "))) {\r
+      if (i < s2.getSequence().length())\r
+        chr2 = s2.getSequence().charAt(i);\r
+      else\r
+        chr2 = '.';\r
+\r
 \r
-        if (!str1.equals(str2)) {\r
+      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))\r
+      {\r
+        if (chr1!=chr2)\r
           bad++;\r
-        }\r
       }\r
     }\r
 \r
     return (float)100*(len-bad)/len;\r
   }\r
+\r
+  public static boolean isGap(char c)\r
+  {\r
+    return  (c != '.' && c != '-' && c != ' ') ? false : true;\r
+  }\r
 }\r