X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=3f0fea0034f6b38c241a38ac4e8519b295d4a4ce;hb=e226ed0ad6ba8552a0b70fb083cf00060588855d;hp=e6181fde7fda57b4b6e84c54aedadd456d8c661b;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index e6181fd..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 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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()
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
- {
- 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();
@@ -127,44 +128,50 @@ public class PIRFile extends AlignFile
// tRNA N3
// other functional RNA N1
- out.append(">N1;" + s[i].getName() + "\n");
+ out.append(">N1;" + s[i].getName());
+ out.append(newline);
if (s[i].getDescription() == null)
{
out.append(s[i].getName() + " "
+ (s[i].getEnd() - s[i].getStart() + 1));
- out.append(is_NA ? " bases\n" : " residues\n");
+ out.append(is_NA ? " bases" : " residues");
+ out.append(newline);
}
else
{
- out.append(s[i].getDescription() + "\n");
+ out.append(s[i].getDescription());
+ out.append(newline);
}
}
else
{
-
if (useModellerOutput)
{
- out.append(">P1;" + s[i].getName() + "\n");
+ out.append(">P1;" + s[i].getName());
+ out.append(newline);
md = new ModellerDescription(s[i]);
- out.append(md.getDescriptionLine() + "\n");
+ out.append(md.getDescriptionLine());
+ out.append(newline);
}
else
{
- out.append(">P1;" + printId(s[i]) + "\n");
+ out.append(">P1;" + printId(s[i], jvsuffix));
+ out.append(newline);
if (s[i].getDescription() != null)
{
- out.append(s[i].getDescription() + "\n");
+ out.append(s[i].getDescription());
+ out.append(newline);
}
else
{
- out
- .append(s[i].getName() + " "
- + (s[i].getEnd() - s[i].getStart() + 1)
- + " residues\n");
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+ out.append(newline);
}
}
}
- int nochunks = (seq.length() / len) + 1;
+ int nochunks = (seq.length() / len)
+ + (seq.length() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
@@ -173,11 +180,13 @@ public class PIRFile extends AlignFile
if (end < seq.length())
{
- out.append(seq.substring(start, end) + "\n");
+ out.append(seq.substring(start, end));
+ out.append(newline);
}
else if (start < seq.length())
{
- out.append(seq.substring(start) + "\n");
+ out.append(seq.substring(start));
+ out.append(newline);
}
}