From cf3ecd2ad13fa9099bba1a21dae4884ed8641fad Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 20 Sep 2013 12:31:23 +0100
Subject: [PATCH] optionally read labels from header of base position plots
---
.../artemis/plot/UserDataAlgorithm.java | 35 +++++++++++++------
1 file changed, 25 insertions(+), 10 deletions(-)
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index 5813c6192..fb4b8b0cb 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -579,7 +579,8 @@ public class UserDataAlgorithm extends BaseAlgorithm
while ((line = reader.readLine()) != null)
{
if((line.indexOf("colour") == -1 &&
- line.indexOf("color") == -1 ) ||
+ line.indexOf("color") == -1 &&
+ line.indexOf("label ") == -1) ||
line.startsWith("track"))
{
if(line.startsWith("track "))
@@ -591,17 +592,31 @@ public class UserDataAlgorithm extends BaseAlgorithm
continue;
}
- int index = line.indexOf("colour");
- if (index == -1)
- index = line.indexOf("color");
+ int idx = line.indexOf("colour");
+ if (idx == -1)
+ idx = line.indexOf("color");
- index = line.indexOf(" ", index + 1);
- line = line.substring(index).trim();
- String rgbValues[] = line.split(" ");
+ if (idx != -1)
+ {
+ idx = line.indexOf(" ", idx + 1);
+ line = line.substring(idx).trim();
+ String rgbValues[] = line.split(" ");
- lines = new LineAttributes[rgbValues.length];
- for (int j = 0; j < rgbValues.length; j++)
- lines[j] = new LineAttributes(LineAttributes.parse(rgbValues[j]));
+ lines = new LineAttributes[rgbValues.length];
+ for (int j = 0; j < rgbValues.length; j++)
+ lines[j] = new LineAttributes(LineAttributes.parse(rgbValues[j]));
+ }
+ else if(lines != null)
+ {
+ idx = line.indexOf("label ");
+ if (idx != -1)
+ {
+ line = line.substring(idx+6).trim();
+ String labels[] = line.split(" ");
+ for (int j = 0; j < labels.length; j++)
+ lines[j].setLabel(labels[j]);
+ }
+ }
}
}
catch (NumberFormatException e)
--
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