X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=0edcb63556fc402b41d1a9fdb3f0d9dcbc0b2657;hb=ef3333028b291ce92bdae34bd2f8487d35d0a0d3;hp=687eef9cacef4f0a7e36bc5215695d9862a8e3e2;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 687eef9..0edcb63 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -25,26 +25,60 @@ import java.io.*;
 import java.util.*;
 
 
-public class BLCFile extends AlignFile {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BLCFile extends AlignFile
+{
     Vector titles;
 
-    public BLCFile() {
+    /**
+     * Creates a new BLCFile object.
+     */
+    public BLCFile()
+    {
     }
 
-    public BLCFile(String inStr) {
+    /**
+     * Creates a new BLCFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public BLCFile(String inStr)
+    {
         super(inStr);
     }
 
-    public BLCFile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new BLCFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public BLCFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public void initData() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void initData()
+    {
         super.initData();
         titles = new Vector();
     }
 
-    public void parse() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void parse()
+    {
         boolean idsFound = false;
         Vector ids = new Vector();
         StringBuffer[] seqstrings;
@@ -53,12 +87,15 @@ public class BLCFile extends AlignFile {
 
         String line = null;
 
-        try {
-            do {
+        try
+        {
+            do
+            {
                 line = nextLine();
 
                 // seek end of ids
-                if (line.indexOf("*") > -1) {
+                if (line.indexOf("*") > -1)
+                {
                     idsFound = true;
 
                     break;
@@ -66,14 +103,16 @@ public class BLCFile extends AlignFile {
 
                 int abracket = line.indexOf(">");
 
-                if (abracket > -1) {
+                if (abracket > -1)
+                {
                     if (line.indexOf(" ") > -1) //
-                     {
+                    {
                         ///Colur it be this format?
                         //>54402046         0             1   137   137:
                         // or this??
                         //     1   >L1H14       30539  343
-                        try {
+                        try
+                        {
                             ids.addElement(line.substring(abracket + 1,
                                     line.indexOf(" ", abracket + 1)));
 
@@ -92,66 +131,106 @@ public class BLCFile extends AlignFile {
                             value = Integer.parseInt(line.substring(0,
                                         line.indexOf(" ")));
                             ends.addElement(value + "");
-                        } catch (Exception ex) {
+                        }
+                        catch (Exception ex)
+                        {
                             System.err.println("Error during blockfile read.");
                             ex.printStackTrace();
-                            starts.addElement("0");
-                            ends.addElement("0");
+                            starts.addElement("1");
+                            ends.addElement("-1");
+                        }
+                    }
+                    else
+                    {
+                        if (line.indexOf("/") > -1)
+                        {
+                            ids.addElement(line.substring(abracket + 1,
+                                    line.indexOf("/")));
+                            line = line.substring(line.indexOf("/") + 1);
+                            starts.addElement(line.substring(0,
+                                    line.indexOf("-")));
+                            ends.addElement(line.substring(line.indexOf("-") +
+                                    1));
+                        }
+                        else
+                        {
+                            ids.addElement(line.substring(abracket + 1));
+                            starts.addElement("1");
+                            ends.addElement("-1");
                         }
-                    } else {
-                        ids.addElement(line.substring(abracket + 1,
-                                line.indexOf("/")));
-                        line = line.substring(line.indexOf("/") + 1);
-                        starts.addElement(line.substring(0, line.indexOf("-")));
-                        ends.addElement(line.substring(line.indexOf("-") + 1));
                     }
                 }
-            } while (!idsFound);
+            }
+            while (!idsFound);
 
             int starCol = line.indexOf("*");
             seqstrings = new StringBuffer[ids.size()];
 
-            for (int i = 0; i < ids.size(); i++) {
-                if (seqstrings[i] == null) {
+            for (int i = 0; i < ids.size(); i++)
+            {
+                if (seqstrings[i] == null)
+                {
                     seqstrings[i] = new StringBuffer();
                 }
             }
 
-            while ((line = nextLine()).indexOf("*") == -1) {
-                for (int i = 0; i < ids.size(); i++) {
-                    if (line.length() > (i + starCol)) {
+            while ((line = nextLine()).indexOf("*") == -1)
+            {
+                for (int i = 0; i < ids.size(); i++)
+                {
+                    if (line.length() > (i + starCol))
+                    {
                         seqstrings[i].append(line.charAt(i + starCol));
                     }
                 }
             }
 
-            for (int i = 0; i < ids.size(); i++) {
+            for (int i = 0; i < ids.size(); i++)
+            {
                 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
                         seqstrings[i].toString(),
                         Integer.parseInt(starts.elementAt(i).toString()),
                         Integer.parseInt(ends.elementAt(i).toString()));
                 seqs.addElement(newSeq);
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
     }
 
-    public String print() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
         return print(getSeqsAsArray());
     }
 
-    public static String print(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s)
+    {
         StringBuffer out = new StringBuffer();
 
         int i = 0;
         int max = -1;
 
-        while ((i < s.length) && (s[i] != null)) {
+        while ((i < s.length) && (s[i] != null))
+        {
             out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +
                 s[i].getEnd() + "\n");
 
-            if (s[i].getSequence().length() > max) {
+            if (s[i].getSequence().length() > max)
+            {
                 max = s[i].getSequence().length();
             }
 
@@ -160,13 +239,18 @@ public class BLCFile extends AlignFile {
 
         out.append("* iteration 1\n");
 
-        for (int j = 0; j < max; j++) {
+        for (int j = 0; j < max; j++)
+        {
             i = 0;
 
-            while ((i < s.length) && (s[i] != null)) {
-                if (s[i].getSequence().length() > j) {
+            while ((i < s.length) && (s[i] != null))
+            {
+                if (s[i].getSequence().length() > j)
+                {
                     out.append(s[i].getSequence().substring(j, j + 1));
-                } else {
+                }
+                else
+                {
                     out.append("-");
                 }