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JAL-3454 tidy comments
[jalview.git]
/
src
/
jalview
/
io
/
PIRFile.java
diff --git
a/src/jalview/io/PIRFile.java
b/src/jalview/io/PIRFile.java
index
adbf81a
..
3f0fea0
100755
(executable)
--- a/
src/jalview/io/PIRFile.java
+++ b/
src/jalview/io/PIRFile.java
@@
-20,24
+20,25
@@
*/
package jalview.io;
*/
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 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()
{
}
- 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
}
public PIRFile(FileParse source) throws IOException
@@
-45,6
+46,7
@@
public class PIRFile extends AlignFile
super(source);
}
super(source);
}
+ @Override
public void parse() throws IOException
{
StringBuffer sequence;
public void parse() throws IOException
{
StringBuffer sequence;
@@
-99,19
+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;
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();
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
@@
-147,7
+145,6
@@
public class PIRFile extends AlignFile
}
else
{
}
else
{
-
if (useModellerOutput)
{
out.append(">P1;" + s[i].getName());
if (useModellerOutput)
{
out.append(">P1;" + s[i].getName());
@@
-158,7
+155,7
@@
public class PIRFile extends AlignFile
}
else
{
}
else
{
- out.append(">P1;" + printId(s[i]));
+ out.append(">P1;" + printId(s[i], jvsuffix));
out.append(newline);
if (s[i].getDescription() != null)
{
out.append(newline);
if (s[i].getDescription() != null)
{
@@
-173,7
+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++)
{
for (int j = 0; j < nochunks; j++)
{