import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import java.awt.Color;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.DataInputStream;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import java.util.StringTokenizer;
import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
*/
Map<String, SequenceI> seqRefIds = null;
- Vector frefedSequence = null;
+ Vector<Object[]> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
int r = 0, rSize = frefedSequence.size();
while (r < rSize)
{
- Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ Object[] ref = frefedSequence.elementAt(r);
if (ref != null)
{
String sref = (String) ref[0];
if (sf[index].otherDetails != null)
{
String key;
- Enumeration keys = sf[index].otherDetails.keys();
- while (keys.hasMoreElements())
+ Iterator<String> keys = sf[index].otherDetails.keySet()
+ .iterator();
+ while (keys.hasNext())
{
- key = keys.nextElement().toString();
+ key = keys.next();
OtherData keyValue = new OtherData();
keyValue.setKey(key);
keyValue.setValue(sf[index].otherDetails.get(key).toString());
// SAVE MAPPINGS
if (jal.getCodonFrames() != null)
{
- Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+ List<AlignedCodonFrame> jac = jal.getCodonFrames();
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
view.setViewName(av.viewName);
view.setGatheredViews(av.isGatherViewsHere());
- Rectangle position = ap.av.getExplodedGeometry();
- if (position == null)
+ Rectangle size = ap.av.getExplodedGeometry();
+ Rectangle position = size;
+ if (size == null)
{
- position = ap.alignFrame.getBounds();
+ size = ap.alignFrame.getBounds();
+ if (av.getCodingComplement() != null)
+ {
+ position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+ .getBounds();
+ }
+ else
+ {
+ position = size;
+ }
}
view.setXpos(position.x);
view.setYpos(position.y);
- view.setWidth(position.width);
- view.setHeight(position.height);
+
+ view.setWidth(size.width);
+ view.setHeight(size.height);
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
.getFeatureRenderer().getRenderOrder()
.toArray(new String[0]);
- Vector settingsAdded = new Vector();
+ Vector<String> settingsAdded = new Vector<String>();
Object gstyle = null;
GraduatedColor gcol = null;
if (renderOrder != null)
{
- for (int ro = 0; ro < renderOrder.length; ro++)
+ for (String featureType : renderOrder)
{
gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
+ .getFeatureStyle(featureType);
Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
+ setting.setType(featureType);
if (gstyle instanceof GraduatedColor)
{
gcol = (GraduatedColor) gstyle;
}
else
{
- setting.setColour(ap.getSeqPanel().seqCanvas
- .getFeatureRenderer().getColour(renderOrder[ro])
- .getRGB());
+ setting.setColour(((Color) gstyle).getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
- renderOrder[ro]));
+ featureType));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ .getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
}
fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ settingsAdded.addElement(featureType);
}
}
- // Make sure we save none displayed feature settings
- Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getFeatureColours().keySet().iterator();
- while (en.hasNext())
- {
- String key = en.next().toString();
- if (settingsAdded.contains(key))
- {
- continue;
- }
-
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getColour(key).getRGB());
-
- setting.setDisplay(false);
- float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getOrder(key);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
- }
- fs.addSetting(setting);
- settingsAdded.addElement(key);
- }
// is groups actually supposed to be a map here ?
- en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ Iterator<String> en = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
.getFeatureGroups().iterator();
- Vector groupsAdded = new Vector();
+ Vector<String> groupsAdded = new Vector<String>();
while (en.hasNext())
{
- String grp = en.next().toString();
+ String grp = en.next();
if (groupsAdded.contains(grp))
{
continue;
}
}
throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam", new Object[]
- { calcIdParam.toString() }));
+ "error.unsupported_version_calcIdparam",
+ new Object[] { calcIdParam.toString() }));
}
/**
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
- if (jds.getDatasetSequence().getDBRef() != null)
+ if (jds.getDatasetSequence().getDBRefs() != null)
{
- dbrefs = jds.getDatasetSequence().getDBRef();
+ dbrefs = jds.getDatasetSequence().getDBRefs();
}
}
else
{
vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
// dataset sequences only
- dbrefs = jds.getDBRef();
+ dbrefs = jds.getDBRefs();
}
if (dbrefs != null)
{
{
SwingUtilities.invokeAndWait(new Runnable()
{
+ @Override
public void run()
{
setLoadingFinishedForNewStructureViewers();
}
if (frefedSequence == null)
{
- frefedSequence = new Vector();
+ frefedSequence = new Vector<Object[]>();
}
AlignFrame af = null, _af = null;
int width = (int) dnaFrame.getBounds().getWidth();
int height = (int) (dnaFrame.getBounds().getHeight()
+ proteinFrame.getBounds().getHeight() + 50);
+
+ /*
+ * SplitFrame location is saved to both enclosed frames
+ */
+ splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
Desktop.addInternalFrame(splitFrame, title, width, height);
/*
{
mapping = addMapping(maps[m].getMapping());
}
- if (dnaseq != null)
+ if (dnaseq != null && mapping.getTo() != null)
{
cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
}
else
{
// defer to later
- frefedSequence.add(new Object[]
- { maps[m].getDnasq(), cf, mapping });
+ frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+ mapping });
}
}
}
* indicate that annotation colours are applied across all groups (pre
* Jalview 2.8.1 behaviour)
*/
- boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
- object.getVersion());
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
+ "2.8.1", object.getVersion());
AlignmentPanel ap = null;
boolean isnewview = true;
}
/**
+ * Answers true if 'version' is equal to or later than 'supported', where each
+ * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+ * changes. Development and test values for 'version' are leniently treated
+ * i.e. answer true.
*
* @param supported
* - minimum version we are comparing against
* @param version
- * - version of data being processsed.
- * @return true if version is development/null or evaluates to the same or
- * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ * - version of data being processsed
+ * @return
*/
- protected boolean isVersionStringLaterThan(String supported,
+ public static boolean isVersionStringLaterThan(String supported,
String version)
{
- if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ if (supported == null || version == null
+ || version.equalsIgnoreCase("DEVELOPMENT BUILD")
|| version.equalsIgnoreCase("Test")
|| version.equalsIgnoreCase("AUTOMATED BUILD"))
{
}
else
{
- StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
- version, ".");
- while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
- {
- // convert b to decimal to catch bugfix releases within a series
- String curT = currentV.nextToken().toLowerCase().replace('b', '.');
- String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
- try
- {
- if (Float.valueOf(curT) > Float.valueOf(fileT))
- {
- // current version is newer than the version that wrote the file
- return false;
- }
- } catch (NumberFormatException nfe)
- {
- System.err
- .println("** WARNING: Version comparison failed for tokens ("
- + curT
- + ") and ("
- + fileT
- + ")\n** Current: '"
- + supported + "' and Version: '" + version + "'");
- }
- }
- if (currentV.hasMoreElements())
- {
- // fileV has no minor version but identical series to current
- return false;
- }
+ return StringUtils.compareVersions(version, supported, "b") >= 0;
}
- return true;
}
Vector<JalviewStructureDisplayI> newStructureViewers = null;
/**
* Kludge for magic autoannotation names (see JAL-811)
*/
- String[] magicNames = new String[]
- { "Consensus", "Quality", "Conservation" };
+ String[] magicNames = new String[] { "Consensus", "Quality",
+ "Conservation" };
JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
for (String nm : magicNames)
}
else
{
- frefedSequence.add(new Object[]
- { dsfor, jmap });
+ frefedSequence.add(new Object[] { dsfor, jmap });
}
}
else
git://source.jalview.org / jalview.git / blobdiff