Formatted source

[jalview.git] / src / jalview / datamodel / BinarySequence.java

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 63c8d86..a351b04 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -16,96 +16,110 @@
 * along with this program; if not, write to the Free Software\r
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
 */\r
-\r
 package jalview.datamodel;\r
 \r
-import jalview.io.*;\r
 import jalview.analysis.PCA;\r
+\r
+import jalview.io.*;\r
+\r
 import jalview.jbgui.*;\r
+\r
 import jalview.schemes.*;\r
 \r
 import java.awt.*;\r
 \r
+\r
 public class BinarySequence extends Sequence {\r
-  int[] binary;\r
-  double[] dbinary;\r
-\r
-  public BinarySequence(SequenceI s) {\r
-    super(s.getName(),s.getSequence(),s.getStart(),s.getEnd());\r
-  }\r
-\r
-  public BinarySequence(String name, String sequence, int start, int end) {\r
-    super(name,sequence,start,end);\r
-  }\r
-\r
-  public void encode() {\r
-    // Set all matrix to 0\r
-    dbinary = new double[getSequence().length() * 21];\r
-    int nores = 21;\r
-    for (int i = 0; i < dbinary.length; i++) {\r
-      dbinary[i] = 0.0;\r
+    int[] binary;\r
+    double[] dbinary;\r
+\r
+    public BinarySequence(SequenceI s) {\r
+        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());\r
+    }\r
+\r
+    public BinarySequence(String name, String sequence, int start, int end) {\r
+        super(name, sequence, start, end);\r
     }\r
 \r
-    for (int i=0; i < getSequence().length(); i++ ) {\r
-      int aanum = 20;\r
-      try {\r
-        aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
-      } catch (NullPointerException e) {\r
-        aanum = 20;\r
-      }\r
-      if (aanum > 20) {\r
-        aanum = 20;\r
-      }\r
+    public void encode() {\r
+        // Set all matrix to 0\r
+        dbinary = new double[getSequence().length() * 21];\r
 \r
-      dbinary[i* nores + aanum] = 1.0;\r
+        int nores = 21;\r
 \r
+        for (int i = 0; i < dbinary.length; i++) {\r
+            dbinary[i] = 0.0;\r
+        }\r
+\r
+        for (int i = 0; i < getSequence().length(); i++) {\r
+            int aanum = 20;\r
+\r
+            try {\r
+                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+                                                                         .substring(i,\r
+                            i + 1))).intValue();\r
+            } catch (NullPointerException e) {\r
+                aanum = 20;\r
+            }\r
+\r
+            if (aanum > 20) {\r
+                aanum = 20;\r
+            }\r
+\r
+            dbinary[(i * nores) + aanum] = 1.0;\r
+        }\r
     }\r
-  }\r
-\r
-  public void blosumEncode() {\r
-\r
-    // Set all matrix to 0\r
-    dbinary = new double[getSequence().length() * 21];\r
-    int nores = 21;\r
-    //for (int i = 0; i < dbinary.length; i++) {\r
-    //  dbinary[i] = 0.0;\r
-    //}\r
-\r
-    for (int i=0; i < getSequence().length(); i++ ) {\r
-      int aanum = 20;\r
-      try {\r
-        aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
-      } catch (NullPointerException e) {\r
-        aanum = 20;\r
-      }\r
-      if (aanum > 20) {\r
-        aanum = 20;\r
-      }\r
-\r
-      // Do the blosum thing\r
-      for (int j = 0;j < 20;j++) {\r
-        dbinary[i * nores + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
-      }\r
 \r
+    public void blosumEncode() {\r
+        // Set all matrix to 0\r
+        dbinary = new double[getSequence().length() * 21];\r
+\r
+        int nores = 21;\r
+\r
+        //for (int i = 0; i < dbinary.length; i++) {\r
+        //  dbinary[i] = 0.0;\r
+        //}\r
+        for (int i = 0; i < getSequence().length(); i++) {\r
+            int aanum = 20;\r
+\r
+            try {\r
+                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+                                                                         .substring(i,\r
+                            i + 1))).intValue();\r
+            } catch (NullPointerException e) {\r
+                aanum = 20;\r
+            }\r
+\r
+            if (aanum > 20) {\r
+                aanum = 20;\r
+            }\r
+\r
+            // Do the blosum thing\r
+            for (int j = 0; j < 20; j++) {\r
+                dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
+            }\r
+        }\r
     }\r
-  }\r
-\r
-  public String toBinaryString() {\r
-    String out = "";\r
-    for (int i=0; i < binary.length;i++) {\r
-      out += (new Integer(binary[i])).toString();\r
-      if (i < binary.length-1) {\r
-        out += " ";\r
-      }\r
+\r
+    public String toBinaryString() {\r
+        String out = "";\r
+\r
+        for (int i = 0; i < binary.length; i++) {\r
+            out += (new Integer(binary[i])).toString();\r
+\r
+            if (i < (binary.length - 1)) {\r
+                out += " ";\r
+            }\r
+        }\r
+\r
+        return out;\r
     }\r
-    return out;\r
-  }\r
 \r
-  public double[] getDBinary() {\r
-    return dbinary;\r
-  }\r
+    public double[] getDBinary() {\r
+        return dbinary;\r
+    }\r
 \r
-  public static void printMemory(Runtime rt) {\r
-    System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
-  }\r
+    public static void printMemory(Runtime rt) {\r
+        System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
+    }\r
 }\r