X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=3f0fea0034f6b38c241a38ac4e8519b295d4a4ce;hb=4b2392caa53f1de3400e7916d1d9c7b815d446f4;hp=9431cc53477e2ca9667933da24155cfdd78da81f;hpb=2bd43f464e725844b02a106c2d2f187c2c3655a6;p=jalview.git
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 9431cc5..3f0fea0 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,40 +1,44 @@
/*
- * 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.bin.Cache;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.io.IOException;
public class PIRFile extends AlignFile
{
- public static boolean useModellerOutput = false;
-
- Vector words = new Vector(); // Stores the words in a line after splitting
+ // Vector words = new Vector(); // Stores the words in a line after splitting
public PIRFile()
{
}
- public PIRFile(String inFile, String type) throws IOException
+ public PIRFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PIRFile(FileParse source) throws IOException
@@ -42,6 +46,7 @@ public class PIRFile extends AlignFile
super(source);
}
+ @Override
public void parse() throws IOException
{
StringBuffer sequence;
@@ -96,19 +101,15 @@ public class PIRFile extends AlignFile
}
}
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
- boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ boolean is_NA = Comparison.isNucleotide(s);
int len = 72;
StringBuffer out = new StringBuffer();
int i = 0;
ModellerDescription md;
-
+ boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
@@ -144,7 +145,6 @@ public class PIRFile extends AlignFile
}
else
{
-
if (useModellerOutput)
{
out.append(">P1;" + s[i].getName());
@@ -155,7 +155,7 @@ public class PIRFile extends AlignFile
}
else
{
- out.append(">P1;" + printId(s[i]));
+ out.append(">P1;" + printId(s[i], jvsuffix));
out.append(newline);
if (s[i].getDescription() != null)
{
@@ -170,7 +170,8 @@ public class PIRFile extends AlignFile
}
}
}
- int nochunks = (seq.length() / len) + 1;
+ int nochunks = (seq.length() / len)
+ + (seq.length() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{