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JAL-1616 loading of datasets from XML patched
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
dfacd54
..
4e72236
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-498,7
+498,7
@@
public class Jalview2XML
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
@@
-1127,7
+1127,7
@@
public class Jalview2XML
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
+ view.setRightAlignIds(av.isRightAlignIds());
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
@@
-1145,11
+1145,11
@@
public class Jalview2XML
view.setFollowHighlight(av.followHighlight);
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
view.setFollowHighlight(av.followHighlight);
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
- if (av.featuresDisplayed != null)
+ if (av.getFeaturesDisplayed() != null)
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
Vector settingsAdded = new Vector();
Object gstyle = null;
Vector settingsAdded = new Vector();
Object gstyle = null;
@@
-1158,7
+1158,7
@@
public class Jalview2XML
{
for (int ro = 0; ro < renderOrder.length; ro++)
{
{
for (int ro = 0; ro < renderOrder.length; ro++)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getFeatureStyle(renderOrder[ro]);
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
.getFeatureStyle(renderOrder[ro]);
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
@@
-1176,13
+1176,13
@@
public class Jalview2XML
}
else
{
}
else
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getColour(renderOrder[ro]).getRGB());
}
.getColour(renderOrder[ro]).getRGB());
}
- setting.setDisplay(av.featuresDisplayed
+ setting.setDisplay(av.getFeaturesDisplayed()
.containsKey(renderOrder[ro]));
.containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(renderOrder[ro]);
if (rorder > -1)
{
.getOrder(renderOrder[ro]);
if (rorder > -1)
{
@@
-1194,7
+1194,7
@@
public class Jalview2XML
}
// Make sure we save none displayed feature settings
}
// Make sure we save none displayed feature settings
- Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
.keySet().iterator();
while (en.hasNext())
{
.keySet().iterator();
while (en.hasNext())
{
@@
-1206,11
+1206,11
@@
public class Jalview2XML
Setting setting = new Setting();
setting.setType(key);
Setting setting = new Setting();
setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getColour(key).getRGB());
setting.setDisplay(false);
.getColour(key).getRGB());
setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(key);
if (rorder > -1)
{
.getOrder(key);
if (rorder > -1)
{
@@
-1219,7
+1219,7
@@
public class Jalview2XML
fs.addSetting(setting);
settingsAdded.addElement(key);
}
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
.keySet().iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
.keySet().iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
@@
-1231,7
+1231,7
@@
public class Jalview2XML
}
Group g = new Group();
g.setName(grp);
}
Group g = new Group();
g.setName(grp);
- g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
.getFeatureRenderer().featureGroups.get(grp))
.booleanValue());
fs.addGroup(g);
.getFeatureRenderer().featureGroups.get(grp))
.booleanValue());
fs.addGroup(g);
@@
-1419,7
+1419,16
@@
public class Jalview2XML
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
-
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
AnnotationElement ae;
if (aa[i].annotations != null)
{
AnnotationElement ae;
if (aa[i].annotations != null)
{
@@
-1447,8
+1456,7
@@
public class Jalview2XML
}
ae.setPosition(a);
}
ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
+ if (aa[i].annotations[a].secondaryStructure > ' ')
{
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
{
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
@@
-2305,7
+2313,10
@@
public class Jalview2XML
}
else
{
}
else
{
- recoverDatasetFor(vamsasSet, al);
+ // recover dataset - passing on flag indicating if this a 'viewless'
+ // sequence set (a.k.a. a stored dataset for the project)
+ recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+ .getViewportCount() == 0);
}
// ///////////////////////////////
}
// ///////////////////////////////
@@
-2631,6
+2642,14
@@
public class Jalview2XML
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
@@
-3455,7
+3474,7
@@
public class Jalview2XML
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.rightAlignIds = view.getRightAlignIds();
+ af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(new java.awt.Font(view.getFontName(), view
.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
af.viewport.setFont(new java.awt.Font(view.getFontName(), view
.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
@@
-3587,7
+3606,7
@@
public class Jalview2XML
// recover featre settings
if (jms.getFeatureSettings() != null)
{
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.featuresDisplayed = new Hashtable();
+ af.viewport.setFeaturesDisplayed(new Hashtable());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
@@
-3616,36
+3635,36
@@
public class Jalview2XML
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
setting.getType(), gc);
}
else
{
setting.getType(), gc);
}
else
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
{
setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(), setting.getOrder());
}
else
{
setting.getType(), setting.getOrder());
}
else
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(),
fs / jms.getFeatureSettings().getSettingCount());
}
if (setting.getDisplay())
{
setting.getType(),
fs / jms.getFeatureSettings().getSettingCount());
}
if (setting.getDisplay())
{
- af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
setting.getColour()));
}
}
setting.getColour()));
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
Hashtable fgtable;
Hashtable fgtable;
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
@@
-3969,7
+3988,8
@@
public class Jalview2XML
}
}
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ boolean ignoreUnrefed)
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
@@
-3981,7
+4001,7
@@
public class Jalview2XML
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
}
// create a new dataset
if (ds == null)
}
// create a new dataset
if (ds == null)
@@
-3994,7
+4014,7
@@
public class Jalview2XML
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
- if (al.getDataset() == null)
+ if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
}
{
al.setDataset(ds);
}
@@
-4010,7
+4030,7
@@
public class Jalview2XML
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
@@
-4021,7
+4041,10
@@
public class Jalview2XML
{
dsq = sq.getDatasetSequence();
}
{
dsq = sq.getDatasetSequence();
}
-
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
+ }
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{