X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=ede258e02512cf6fd21d9c99dcf253e8d743861a;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f489d805f7b66d1c822b41356f9836091720c36d;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index f489d80..ede258e 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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;
@@ -33,10 +35,10 @@ package jalview.io;
* found in Emboss (thanks David Martin!)
*
*/
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
public class PileUpfile extends MSFfile
{
@@ -53,15 +55,16 @@ public class PileUpfile extends MSFfile
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public PileUpfile(String inFile, String type) throws IOException
+ public PileUpfile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PileUpfile(FileParse source) throws IOException
@@ -69,17 +72,8 @@ public class PileUpfile extends MSFfile
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);
@@ -98,8 +92,8 @@ public class PileUpfile extends MSFfile
i++;
}
- out.append(" MSF: " + s[0].getSequence().length
- + " Type: P Check: " + bigChecksum % 10000 + " ..");
+ out.append(" MSF: " + s[0].getLength() + " Type: P Check: "
+ + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
out.append(newline);
@@ -108,8 +102,9 @@ 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()
- + " Check: " + checksums[i] + " Weight: 1.00");
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length() + " Check: " + checksums[i]
+ + " Weight: 1.00");
out.append(newline);
if (seq.length() > max)
@@ -139,12 +134,7 @@ public class PileUpfile extends MSFfile
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++)
{
@@ -152,7 +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 + " "));
@@ -161,8 +151,8 @@ public class PileUpfile extends MSFfile
int start = (i * 50) + (k * 10);
int end = start + 10;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
@@ -177,7 +167,7 @@ public class PileUpfile extends MSFfile
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);