X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=84be72ceb4416c3d5815abfef60de041f0cb0cad;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=4fb4ee7f5daade4fee0b5b2929bcca9ba81905af;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 4fb4ee7..84be72c 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
@@ -32,19 +35,10 @@ package jalview.io;
* found in Emboss (thanks David Martin!)
*
*/
-import java.io.*;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-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 jalview.util.*;
+import java.io.IOException;
public class PileUpfile extends MSFfile
{
@@ -61,45 +55,30 @@ public class PileUpfile extends MSFfile
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PileUpfile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
- public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PileUpfile(FileParse source) throws IOException
{
super(source);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
out.append(newline);
-
+
int max = 0;
int maxid = 0;
@@ -114,8 +93,7 @@ public class PileUpfile extends MSFfile
}
out.append(" MSF: " + s[0].getSequence().length
- + " Type: P Check: " + bigChecksum % 10000
- + " ..");
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
out.append(newline);
@@ -124,7 +102,8 @@ public class PileUpfile extends MSFfile
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
- out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length()
+ " Check: " + checksums[i] + " Weight: 1.00");
out.append(newline);
@@ -147,17 +126,15 @@ public class PileUpfile extends MSFfile
}
maxid++;
- out.append(newline);out.append(newline);out.append("//");
- out.append(newline);out.append(newline);
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
int len = 50;
- int nochunks = (max / len) + 1;
-
- if ((max % len) == 0)
- {
- nochunks--;
- }
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{
@@ -165,7 +142,7 @@ public class PileUpfile extends MSFfile
while ((j < s.length) && (s[j] != null))
{
- String name = printId(s[j]);
+ String name = printId(s[j], jvsuffix);
out.append(new Format("%-" + maxid + "s").form(name + " "));