X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=0edcb63556fc402b41d1a9fdb3f0d9dcbc0b2657;hb=3ca1aeccca8d3adfd55d1ff8bd447f8bf0d4ac2f;hp=7961810c33c927c360700a62d7953173064d1167;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 7961810..0edcb63 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -16,160 +16,252 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.io;
 
 import jalview.datamodel.*;
 
 import java.io.*;
+
 import java.util.*;
 
-public class BLCFile extends AlignFile {
 
-  Vector titles;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BLCFile extends AlignFile
+{
+    Vector titles;
+
+    /**
+     * Creates a new BLCFile object.
+     */
+    public BLCFile()
+    {
+    }
+
+    /**
+     * Creates a new BLCFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public BLCFile(String inStr)
+    {
+        super(inStr);
+    }
+
+    /**
+     * 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);
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void initData()
+    {
+        super.initData();
+        titles = new Vector();
+    }
 
-  public BLCFile()
-  {}
+    /**
+     * DOCUMENT ME!
+     */
+    public void parse()
+    {
+        boolean idsFound = false;
+        Vector ids = new Vector();
+        StringBuffer[] seqstrings;
+        Vector starts = new Vector();
+        Vector ends = new Vector();
 
-  public BLCFile(String inStr) {
-    super(inStr);
-  }
+        String line = null;
 
-  public void initData() {
-    super.initData();
-    titles = new Vector();
-  }
+        try
+        {
+            do
+            {
+                line = nextLine();
 
-  public BLCFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
+                // seek end of ids
+                if (line.indexOf("*") > -1)
+                {
+                    idsFound = true;
 
+                    break;
+                }
 
-  public void parse()
-  {
-    boolean idsFound=false;
-    Vector ids = new Vector();
-    StringBuffer seqstrings [];
-    Vector starts = new Vector();
-    Vector ends = new Vector();
+                int abracket = line.indexOf(">");
 
-   String line=null;
-   try{
-     do{
-      line = nextLine();
+                if (abracket > -1)
+                {
+                    if (line.indexOf(" ") > -1) //
+                    {
+                        ///Colur it be this format?
+                        //>54402046         0             1   137   137:
+                        // or this??
+                        //     1   >L1H14       30539  343
+                        try
+                        {
+                            ids.addElement(line.substring(abracket + 1,
+                                    line.indexOf(" ", abracket + 1)));
 
-      // seek end of ids
-      if (line.indexOf("*") > -1)
-      {
-        idsFound=true;
-        break;
-      }
+                            // remove p Value
+                            line = line.substring(abracket + 1);
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
 
-      int abracket = line.indexOf(">");
+                            int value = Integer.parseInt(line.substring(0,
+                                        line.indexOf(" ")));
+                            starts.addElement(value + "");
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
+                            value = Integer.parseInt(line.substring(0,
+                                        line.indexOf(" ")));
+                            ends.addElement(value + "");
+                        }
+                        catch (Exception ex)
+                        {
+                            System.err.println("Error during blockfile read.");
+                            ex.printStackTrace();
+                            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");
+                        }
+                    }
+                }
+            }
+            while (!idsFound);
 
-      if (abracket > -1)
-      {
+            int starCol = line.indexOf("*");
+            seqstrings = new StringBuffer[ids.size()];
 
-        if(line.indexOf(" ")>-1)//
-        {
-          ///Colur it be this format?
-          //>54402046         0             1   137   137:
-          // or this??
-          //     1   >L1H14       30539  343
-          try{
-            ids.addElement(line.substring(abracket + 1,
-                                          line.indexOf(" ", abracket + 1)));
-
-
-            // remove p Value
-            line = line.substring(abracket + 1);
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
-            starts.addElement(value+"");
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
-            ends.addElement(value+"");
-
-          }catch(Exception ex)
-          {
-            System.err.println("Error during blockfile read.");
-            ex.printStackTrace();
-            starts.addElement("0");
-            ends.addElement("0");
-          }
+            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))
+                    {
+                        seqstrings[i].append(line.charAt(i + starCol));
+                    }
+                }
+            }
+
+            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);
+            }
         }
-        else
+        catch (Exception ex)
         {
-          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));
+            ex.printStackTrace();
         }
-      }
-    }while(!idsFound);
-
-    int starCol = line.indexOf("*");
-    seqstrings = new StringBuffer[ids.size()];
-    for(int i=0; i<ids.size(); i++)
-    {
-      if(seqstrings[i]==null)
-        seqstrings[i] = new StringBuffer();
     }
 
-    while ((line = nextLine()).indexOf("*")==-1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
     {
-      for(int i=0; i<ids.size(); i++)
-      {
-        if(line.length()>i+starCol)
-          seqstrings[i].append(line.charAt(i + starCol));
-      }
+        return print(getSeqsAsArray());
     }
 
-    for(int i=0; i<ids.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s)
     {
-      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);
-    }
+        StringBuffer out = new StringBuffer();
 
-   }catch(Exception ex){ex.printStackTrace();}
-  }
-
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-  public static String print(SequenceI[] s) {
-    StringBuffer out = new StringBuffer();
-
-    int i=0;
-    int max = -1;
-    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) { max = s[i].getSequence().length();}
-      i++;
-    }
+        int i = 0;
+        int max = -1;
+
+        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)
+            {
+                max = s[i].getSequence().length();
+            }
 
-      out.append("* iteration 1\n");
-      for (int j = 0; j < max; j++) {
-        i=0;
-        while (i < s.length && s[i] != null) {
-          if(s[i].getSequence().length()>j )
-            out.append(s[i].getSequence().substring(j,j+1));
-          else
-            out.append("-");
-          i++;
+            i++;
         }
-        out.append("\n");
-      }
-    out.append("*\n");
-    return out.toString();
 
-  }
+        out.append("* iteration 1\n");
+
+        for (int j = 0; j < max; j++)
+        {
+            i = 0;
+
+            while ((i < s.length) && (s[i] != null))
+            {
+                if (s[i].getSequence().length() > j)
+                {
+                    out.append(s[i].getSequence().substring(j, j + 1));
+                }
+                else
+                {
+                    out.append("-");
+                }
+
+                i++;
+            }
+
+            out.append("\n");
+        }
+
+        out.append("*\n");
+
+        return out.toString();
+    }
 }