From 2c56ea5abe1fa29c861beb02fb594ad807b307ed Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 5 Oct 2005 12:34:32 +0000 Subject: [PATCH] Sequence start end added for the time being --- src/jalview/io/MSFfile.java | 12 ++++++++++-- src/jalview/io/PileUpfile.java | 9 +++++++-- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 8082ee3..2cef0fe 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -316,7 +316,11 @@ public class MSFfile extends AlignFile i=0; while ((i < s.length) && (s[i] != null)) { - nameBlock[i] = new String(" Name: " + s[i].getName() + " "); + + nameBlock[i] = new String(" Name: " + s[i].getName() + + "/" + s[i].getStart() + "-" + s[i].getEnd() + +" "); + idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + " Check: " + maxChkpad.form(checksums[i]) + " Weight: 1.00\n"); @@ -370,7 +374,11 @@ public class MSFfile extends AlignFile while ((j < s.length) && (s[j] != null)) { String name = s[j].getName(); - out.append(new Format("%-" + maxid + "s").form(name)+ " "); + // out.append(new Format("%-" + maxid + "s").form(name)+ " "); + + out.append(new Format("%-" + maxid + "s").form(name + + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " "); + for (int k = 0; k < 5; k++) { diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index 87a1652..8c8a3ea 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -217,7 +217,9 @@ public class PileUpfile while ( (i < s.length) && (s[i] != null)) { String seq = s[i].getSequence(); - out.append(" Name: " + s[i].getName() + " oo Len: " + + out.append(" Name: " + s[i].getName() + + "/" + s[i].getStart() + "-" + s[i].getEnd() + + " oo Len: " + s[i].getSequence().length() + " Check: " + checksums[i] + " Weight: 1.00\n"); @@ -258,7 +260,10 @@ public class PileUpfile while ( (j < s.length) && (s[j] != null)) { String name = s[j].getName(); - out.append(new Format("%-" + maxid + "s").form(name) + " "); + // out.append(new Format("%-" + maxid + "s").form(name) + " "); + + out.append(new Format("%-" + maxid + "s").form(name + + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " "); for (int k = 0; k < 5; k++) { -- 1.7.10.2