X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=71ebbb3f87daff70034c35427fc428fa7dd1e7fc;hb=16359e92bebc20edafc4958b7b580c8ceedd4d37;hp=c9a623b8456a0363c73907765f8486c217d6eac6;hpb=c3583f7ab67ddb450f61af4d36af839ddf485a09;p=jalview.git
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index c9a623b..71ebbb3 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.datamodel;
@@ -66,6 +69,7 @@ public class Annotation
description = desc;
secondaryStructure = ss;
value = val;
+
}
/**
@@ -103,12 +107,17 @@ public class Annotation
return;
}
if (that.displayCharacter != null)
+ {
displayCharacter = new String(that.displayCharacter);
+ }
if (that.description != null)
+ {
description = new String(that.description);
+ }
secondaryStructure = that.secondaryStructure;
value = that.value;
colour = that.colour;
+
}
/**
@@ -119,9 +128,18 @@ public class Annotation
*/
public Annotation(float val)
{
- this(null, null, ' ', val);
+ this(null, null, ' ', val, null);
}
+ /**
+ * human readable representation of an annotation row element.
+ *
+ * Format is 'display Char','secondary Structure
+ * Char',"description",score,[colourstring]
+ *
+ * fields may be missing if they are null, whitespace, or equivalent to
+ * Float.NaN
+ */
@Override
public String toString()
{
@@ -154,7 +172,7 @@ public class Annotation
{
sb.append(",");
}
- if (value != Float.NaN)
+ if (!Float.isNaN(value))
{
sb.append(value);
}