X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=1b938923ed8a079565b2d8c19b8386be62a08b76;hb=94ca0419cc7afa75b3c51917a8beaf46a7c05540;hp=71c95b50c1c2d434008949a9bda17b12ab0109a7;hpb=1a8f953dd71a9e319e910261927f269d69b4692c;p=jalview.git
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 71c95b5..1b93892 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,35 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -53,16 +48,19 @@ public class BLCFile extends AlignFile
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
- * @throws Exception
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public BLCFile(String inFile, String type) throws Exception
+ public BLCFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
- public BLCFile(FileParse source) throws Exception
+ public BLCFile(FileParse source) throws IOException
{
super(source);
}
@@ -70,6 +68,7 @@ public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
@@ -92,6 +91,7 @@ public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer headerLines = new StringBuffer();
@@ -119,7 +119,9 @@ public class BLCFile extends AlignFile
{
line = nextLine();
if (line == null)
+ {
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
@@ -154,7 +156,9 @@ public class BLCFile extends AlignFile
}
} while (!idsFound);
if (line == null)
+ {
break; // end of file.
+ }
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
@@ -202,9 +206,11 @@ public class BLCFile extends AlignFile
}
if (seqs.size() > 0)
{
- if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
// just whitespace or not.
setAlignmentProperty("Comments", headerLines.toString());
+ }
setAlignmentProperty("iteration", "" + iterationCount);
}
}
@@ -212,22 +218,13 @@ public class BLCFile extends AlignFile
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- /**
- * DOCUMENT ME!
- *
* @param s
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer();
/**
@@ -241,7 +238,7 @@ public class BLCFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
- out.append(">" + printId(s[i]));
+ out.append(">" + printId(s[i], jvsuffix));
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
@@ -249,10 +246,7 @@ public class BLCFile extends AlignFile
out.append(newline);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
i++;
}