+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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
*
* TODO refactor to Jalview 'utilities' somehow.
*/
public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features)
+ List<SequenceFeature> features)
{
appendFeatures(tooltipText2, rpos, features, null);
}
public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features, Hashtable minmax)
+ List<SequenceFeature> 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("<br>");
}
- tooltipText2.append("disulfide bond " + features[i].getBegin()
- + ":" + features[i].getEnd());
+ tooltipText2.append("disulfide bond " + feature.getBegin()
+ + ":" + feature.getEnd());
}
}
else
tooltipText2.append("<br>");
}
// 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("<HTML>");
if (startTag > -1)
}
}
// 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)
{
}
else
{
- for (String urlstring : (Vector<String>) features[i].links)
+ for (String urlstring : feature.links)
{
try
{
for (String[] urllink : createLinksFrom(null, urlstring))
{
- tooltipText2.append("<br/> <a href=\"" + urllink[3]
- + "\" target=\"" + urllink[0] + "\">"
- + (urllink[0].toLowerCase().equals(urllink[1].toLowerCase()) ? urllink[0] : (urllink[0]+ ":" + urllink[1])) + "</a></br>");
+ tooltipText2.append("<br/> <a href=\""
+ + urllink[3]
+ + "\" target=\""
+ + urllink[0]
+ + "\">"
+ + (urllink[0].toLowerCase().equals(
+ urllink[1].toLowerCase()) ? urllink[0]
+ : (urllink[0] + ":" + urllink[1]))
+ + "</a></br>");
}
} catch (Exception x)
{
public String[][] createLinksFrom(SequenceI seq, String link)
{
ArrayList<String[]> urlSets = new ArrayList<String[]>();
- ArrayList<String> uniques=new ArrayList<String>();
+ ArrayList<String> uniques = new ArrayList<String>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
// 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();
{
for (int u = 0; u < urls.length; u += 2)
{
- String unq=urls[u]+"|"+urls[u+1];
+ 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);
}
}
{
for (int u = 0; u < urls.length; u += 2)
{
- String unq=urls[u]+"|"+urls[u+1];
+ 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);
}
}
{
for (int u = 0; u < urls.length; u += 2)
{
- String unq=urls[u]+"|"+urls[u+1];
+ 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);
}
}
}
}
- } else {
- String unq=label + "|" + urlLink.getUrl_prefix();
- if (!uniques.contains(unq)){
+ }
+ else
+ {
+ String unq = label + "|" + urlLink.getUrl_prefix();
+ if (!uniques.contains(unq))
+ {
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,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
Hashtable minmax)
{
- createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats, true, minmax);
+ createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
+ true, minmax);
}
public void createSequenceAnnotationReport(final StringBuffer tip,
- SequenceI sequence, boolean showDbRefs, boolean showNpFeats, boolean tableWrap,
- Hashtable minmax)
+ SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
+ boolean tableWrap, Hashtable minmax)
{
String tmp;
tip.append("<i>");
tip.append("<br>" + tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
- SequenceI ds=sequence;
- while (ds.getDatasetSequence()!=null)
+ SequenceI ds = sequence;
+ while (ds.getDatasetSequence() != null)
{
- ds=ds.getDatasetSequence();
+ ds = ds.getDatasetSequence();
}
DBRefEntry[] dbrefs = ds.getDBRef();
if (showDbRefs && dbrefs != null)
}
// 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++)
if (features[i].begin == 0 && features[i].end == 0)
{
int sz = -tip.length();
- tfeat[0] = features[i];
+ List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
+ tfeat.add(features[i]);
appendFeatures(tip, 0, tfeat, minmax);
sz += tip.length();
maxWidth = Math.max(maxWidth, sz);
git://source.jalview.org / jalview.git / blobdiff