X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=e41b38607f3ae99e22a83ed9702376165fdad05d;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=fbcc436d5fabee96df0172ade97ac324d056dde9;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index fbcc436..e41b386 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -1,32 +1,34 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.UrlLink;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
/**
* generate HTML reports for a sequence
*
@@ -52,30 +54,29 @@ public class SequenceAnnotationReport
* TODO refactor to Jalview 'utilities' somehow.
*/
public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features)
+ List features)
{
appendFeatures(tooltipText2, rpos, features, null);
}
public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features, Hashtable minmax)
+ List features, Hashtable minmax)
{
String tmpString;
if (features != null)
{
- for (int i = 0; i < features.length; i++)
+ for (SequenceFeature feature : features)
{
- if (features[i].getType().equals("disulfide bond"))
+ if (feature.getType().equals("disulfide bond"))
{
- if (features[i].getBegin() == rpos
- || features[i].getEnd() == rpos)
+ if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
if (tooltipText2.length() > 6)
{
tooltipText2.append("
");
}
- tooltipText2.append("disulfide bond " + features[i].getBegin()
- + ":" + features[i].getEnd());
+ tooltipText2.append("disulfide bond " + feature.getBegin()
+ + ":" + feature.getEnd());
}
}
else
@@ -85,25 +86,24 @@ public class SequenceAnnotationReport
tooltipText2.append("
");
}
// TODO: remove this hack to display link only features
- boolean linkOnly = features[i].getValue("linkonly") != null;
+ boolean linkOnly = feature.getValue("linkonly") != null;
if (!linkOnly)
{
- tooltipText2.append(features[i].getType() + " ");
+ tooltipText2.append(feature.getType() + " ");
if (rpos != 0)
{
// we are marking a positional feature
- tooltipText2.append(features[i].begin);
+ tooltipText2.append(feature.begin);
}
- if (features[i].begin != features[i].end)
+ if (feature.begin != feature.end)
{
- tooltipText2.append(" " + features[i].end);
+ tooltipText2.append(" " + feature.end);
}
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i]
- .getType()))
+ if (feature.getDescription() != null
+ && !feature.description.equals(feature.getType()))
{
- tmpString = features[i].getDescription();
+ tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("");
if (startTag > -1)
@@ -148,27 +148,27 @@ public class SequenceAnnotationReport
}
}
// check score should be shown
- if (features[i].getScore() != Float.NaN)
+ if (!Float.isNaN(feature.getScore()))
{
float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(features[i].getType()));
+ .get(feature.getType()));
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- tooltipText2.append(" Score=" + features[i].getScore());
+ tooltipText2.append(" Score=" + feature.getScore());
}
}
- if (features[i].getValue("status") != null)
+ if (feature.getValue("status") != null)
{
- String status = features[i].getValue("status").toString();
+ String status = feature.getValue("status").toString();
if (status.length() > 0)
{
- tooltipText2.append("; (" + features[i].getValue("status")
+ tooltipText2.append("; (" + feature.getValue("status")
+ ")");
}
}
}
}
- if (features[i].links != null)
+ if (feature.links != null)
{
if (linkImageURL != null)
{
@@ -176,7 +176,7 @@ public class SequenceAnnotationReport
}
else
{
- for (String urlstring : (Vector) features[i].links)
+ for (String urlstring : feature.links)
{
try
{
@@ -231,8 +231,7 @@ public class SequenceAnnotationReport
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
- new String[]
- { target });
+ new String[] { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
@@ -259,8 +258,8 @@ public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
@@ -278,8 +277,8 @@ public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
@@ -296,8 +295,8 @@ public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
@@ -312,13 +311,12 @@ public class SequenceAnnotationReport
{
uniques.add(unq);
// Add a non-dynamic link
- urlSets.add(new String[]
- { target, label, null, urlLink.getUrl_prefix() });
+ urlSets.add(new String[] { target, label, null,
+ urlLink.getUrl_prefix() });
}
}
- return urlSets.toArray(new String[][]
- {});
+ return urlSets.toArray(new String[][] {});
}
public void createSequenceAnnotationReport(final StringBuffer tip,
@@ -361,8 +359,7 @@ public class SequenceAnnotationReport
}
// ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = ds.getSequenceFeatures();
- SequenceFeature[] tfeat = new SequenceFeature[1];
+ SequenceFeature[] features = sequence.getSequenceFeatures();
if (showNpFeats && features != null)
{
for (int i = 0; i < features.length; i++)
@@ -370,7 +367,8 @@ public class SequenceAnnotationReport
if (features[i].begin == 0 && features[i].end == 0)
{
int sz = -tip.length();
- tfeat[0] = features[i];
+ List tfeat = new ArrayList();
+ tfeat.add(features[i]);
appendFeatures(tip, 0, tfeat, minmax);
sz += tip.length();
maxWidth = Math.max(maxWidth, sz);