import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.Alcodon;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
*/
public class Jalview2XML
{
-
- /**
- * A data bean to hold stored data about a structure viewer.
- */
- public class ViewerData
- {
-
- private int x;
-
- private int y;
-
- private int width;
-
- private int height;
-
- public boolean alignWithPanel;
-
- public boolean colourWithAlignPanel;
-
- public boolean colourByViewer;
-
- String stateData = "";
-
- // todo: java bean in place of Object []
- private Map<File, Object[]> fileData = new HashMap<File, Object[]>();
-
- public ViewerData(int x, int y, int width, int height,
- boolean alignWithPanel, boolean colourWithAlignPanel,
- boolean colourByViewer)
- {
- this.x = x;
- this.y = y;
- this.width = width;
- this.height = height;
- this.alignWithPanel = alignWithPanel;
- this.colourWithAlignPanel = colourWithAlignPanel;
- this.colourByViewer = colourByViewer;
- }
-
- }
-
/*
* SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
* of sequence objects are created.
view.setFontSize(av.font.getSize());
view.setFontStyle(av.font.getStyle());
view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setRightAlignIds(av.isRightAlignIds());
- view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
view.setWrapAlignment(av.getWrapAlignment());
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getRenderOrder().toArray(new String[0]);
Vector settingsAdded = new Vector();
Object gstyle = null;
.getColour(renderOrder[ro]).getRGB());
}
- setting.setDisplay(av.getFeaturesDisplayed()
- .containsKey(renderOrder[ro]));
+ setting.setDisplay(av.getFeaturesDisplayed().isVisible(
+ renderOrder[ro]));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(renderOrder[ro]);
if (rorder > -1)
}
// Make sure we save none displayed feature settings
- Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
- .keySet().iterator();
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureColours().keySet().iterator();
while (en.hasNext())
{
String key = en.next().toString();
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
- .keySet().iterator();
+ // is groups actually supposed to be a map here ?
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups()
+ .iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
{
Group g = new Group();
g.setName(grp);
g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
+ .getFeatureRenderer().checkGroupVisibility(grp, false))
.booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
.size(); c++)
{
- int[] region = (int[]) av.getColumnSelection()
- .getHiddenColumns().elementAt(c);
+ int[] region = av.getColumnSelection()
+ .getHiddenColumns().get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
an.addProperty(prop);
}
}
+
AnnotationElement ae;
if (aa[i].annotations != null)
{
protected void loadStructures(jarInputStreamProvider jprovider,
JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
{
- // run through all PDB ids on the alignment, and collect mappings between
- // jmol view ids and all sequences referring to it
- Map<String, ViewerData> jmolViewIds = new HashMap<String, ViewerData>();
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
for (int i = 0; i < jseqs.length; i++)
{
sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ "," + height;
}
- if (!jmolViewIds.containsKey(sviewid))
+ if (!structureViewers.containsKey(sviewid))
{
- jmolViewIds.put(sviewid, new ViewerData(x, y, width, height,
+ structureViewers.put(sviewid, new StructureViewerModel(x, y, width, height,
false, false, true));
// Legacy pre-2.7 conversion JAL-823 :
// do not assume any view has to be linked for colour by
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}, boolean[] {
// linkAlignPanel,superposeWithAlignpanel}} from hash
- ViewerData jmoldat = jmolViewIds.get(sviewid);
- jmoldat.alignWithPanel |= structureState
- .hasAlignwithAlignPanel() ? structureState.getAlignwithAlignPanel() : false;
- // never colour by linked panel if not specified
- jmoldat.colourWithAlignPanel |= structureState
- .hasColourwithAlignPanel() ? structureState.getColourwithAlignPanel()
- : false;
- // default for pre-2.7 projects is that Jmol colouring is enabled
- jmoldat.colourByViewer &= structureState
+ StructureViewerModel jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ | (structureState.hasAlignwithAlignPanel() ? structureState
+ .getAlignwithAlignPanel() : false));
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= (structureState
+ .hasColourwithAlignPanel() ? structureState
+ .getColourwithAlignPanel() : false);
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState
.hasColourByJmol() ? structureState
.getColourByJmol() : true;
+ jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.stateData.length() < structureState.getContent()
- .length())
+ if (jmoldat.getStateData().length() < structureState
+ .getContent().length())
{
{
- jmoldat.stateData = structureState.getContent();
+ jmoldat.setStateData(structureState.getContent());
}
}
if (ids[p].getFile() != null)
{
File mapkey = new File(ids[p].getFile());
- Object[] seqstrmaps = jmoldat.fileData.get(mapkey);
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
if (seqstrmaps == null)
{
- jmoldat.fileData.put(mapkey,
- seqstrmaps = new Object[]
- { pdbFile, ids[p].getId(), new Vector(),
- new Vector() });
+ jmoldat.getFileData().put(
+ mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ ids[p].getId()));
}
- if (!((Vector) seqstrmaps[2]).contains(seq))
+ if (!seqstrmaps.getSeqList().contains(seq))
{
- ((Vector) seqstrmaps[2]).addElement(seq);
- // ((Vector)seqstrmaps[3]).addElement(n) :
- // in principle, chains
- // should be stored here : do we need to
- // TODO: store and recover seq/pdb_id :
- // chain mappings
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
}
}
else
}
}
// Instantiate the associated structure views
- for (Entry<String, ViewerData> entry : jmolViewIds.entrySet())
+ for (Entry<String, StructureViewerModel> entry : structureViewers.entrySet())
{
createOrLinkStructureViewer(entry, af, ap);
}
* @param ap
*/
protected void createOrLinkStructureViewer(
- Entry<String, ViewerData> viewerData, AlignFrame af,
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
AlignmentPanel ap)
{
- final ViewerData svattrib = viewerData.getValue();
+ final StructureViewerModel svattrib = viewerData.getValue();
/*
* Search for any viewer windows already open from other alignment views
* Pending an XML element for ViewerType, just check if stateData contains
* "chimera" (part of the chimera session filename).
*/
- if (svattrib.stateData.indexOf("chimera") > -1)
+ if (svattrib.getStateData().indexOf("chimera") > -1)
{
createChimeraViewer(viewerData, af);
}
* @param viewerData
* @param af
*/
- protected void createChimeraViewer(Entry<String, ViewerData> viewerData,
+ protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
AlignFrame af)
{
- final ViewerData data = viewerData.getValue();
- String chimeraSession = data.stateData;
- List<String> pdbfilenames = new ArrayList<String>();
- List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
- List<String> pdbids = new ArrayList<String>();
+ final StructureViewerModel data = viewerData.getValue();
+ String chimeraSession = data.getStateData();
if (new File(chimeraSession).exists())
{
- Set<Entry<File, Object[]>> fileData = data.fileData.entrySet();
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
- for (Entry<File, Object[]> pdb : fileData)
- {
- String filePath = (String) pdb.getValue()[0];
- String pdbId = (String) pdb.getValue()[1];
- final Vector seqList = (Vector) pdb.getValue()[2];
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(filePath);
- pdbentry.setId(pdbId);
- pdbs.add(pdbentry);
- SequenceI[] seqs = new SequenceI[seqList.size()];
- seqList.copyInto(seqs);
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ pdbs.add(new PDBEntry(filePath, pdbId));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
allseqs.add(seqs);
}
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
// TODO can/should this be done via StructureViewer (like Jmol)?
final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs
.size()]);
final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs.size()][]);
- ChimeraViewFrame cvf = // new ChimeraViewFrame(data, af);
- new ChimeraViewFrame(af.alignPanel, pdbArray, seqsArray);
+ new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
+ seqsArray,
+ colourByChimera, colourBySequence);
}
else
{
* @param af
*/
protected void createJmolViewer(
- final Entry<String, ViewerData> viewerData, AlignFrame af)
+ final Entry<String, StructureViewerModel> viewerData, AlignFrame af)
{
- final ViewerData svattrib = viewerData.getValue();
- String state = svattrib.stateData;
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
List<String> pdbfilenames = new ArrayList<String>();
List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
List<String> pdbids = new ArrayList<String>();
StringBuilder newFileLoc = new StringBuilder(64);
int cp = 0, ncp, ecp;
- Map<File, Object[]> oldFiles = svattrib.fileData;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
while ((ncp = state.indexOf("load ", cp)) > -1)
{
do
// have to normalize filename - since Jmol and jalview do
// filename
// translation differently.
- Object[] filedat = oldFiles.get(new File(oldfilenam));
- newFileLoc.append(Platform.escapeString((String) filedat[0]));
- pdbfilenames.add((String) filedat[0]);
- pdbids.add((String) filedat[1]);
- seqmaps.add(((Vector<SequenceI>) filedat[2])
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
.toArray(new SequenceI[0]));
newFileLoc.append("\"");
cp = ecp + 1; // advance beyond last \" and set cursor so we can
{
// add this and any other pdb files that should be present in
// the viewer
- Object[] filedat = oldFiles.get(id);
- String nfilename;
- newFileLoc.append(((String) filedat[0]));
- pdbfilenames.add((String) filedat[0]);
- pdbids.add((String) filedat[1]);
- seqmaps.add(((Vector<SequenceI>) filedat[2])
+ StructureData filedat = oldFiles.get(id);
+ newFileLoc.append(filedat.getFilePath());
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
.toArray(new SequenceI[0]));
newFileLoc.append(" \"");
- newFileLoc.append((String) filedat[0]);
+ newFileLoc.append(filedat.getFilePath());
newFileLoc.append("\"");
}
final String fileloc = newFileLoc.toString();
final String sviewid = viewerData.getKey();
final AlignFrame alf = af;
- final java.awt.Rectangle rect = new java.awt.Rectangle(svattrib.x,
- svattrib.y, svattrib.width, svattrib.height);
+ final Rectangle rect = new Rectangle(svattrib.getX(),
+ svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
try
{
javax.swing.SwingUtilities.invokeAndWait(new Runnable()
* @return
*/
protected StructureViewerBase findMatchingViewer(
- Entry<String, ViewerData> viewerData)
+ Entry<String, StructureViewerModel> viewerData)
{
final String sviewid = viewerData.getKey();
- final ViewerData svattrib = viewerData.getValue();
+ final StructureViewerModel svattrib = viewerData.getValue();
StructureViewerBase comp = null;
JInternalFrame[] frames = getAllFrames();
for (JInternalFrame frame : frames)
/*
* Otherwise test for matching position and size of viewer frame
*/
- else if (frame.getX() == svattrib.x && frame.getY() == svattrib.y
- && frame.getHeight() == svattrib.height
- && frame.getWidth() == svattrib.width)
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
{
comp = (AppJmol) frame;
// todo: break?
* @param viewerColouring
*/
protected void linkStructureViewer(AlignmentPanel ap,
- StructureViewerBase viewer, ViewerData svattrib)
+ StructureViewerBase viewer, StructureViewerModel svattrib)
{
// NOTE: if the jalview project is part of a shared session then
// view synchronization should/could be done here.
- final boolean useinViewerSuperpos = svattrib.alignWithPanel;
- final boolean usetoColourbyseq = svattrib.colourWithAlignPanel;
- final boolean viewerColouring = svattrib.colourByViewer;
- Map<File, Object[]> oldFiles = svattrib.fileData;
+ final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
+ final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
+ final boolean viewerColouring = svattrib.isColourByViewer();
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
/*
* Add mapping for sequences in this view to an already open viewer
{
// add this and any other pdb files that should be present in the
// viewer
- Object[] filedat = oldFiles.get(id);
- String pdbFile = (String) filedat[0];
- SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]);
- binding
- .getSsm()
- .setMapping(seq, null, pdbFile,
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
binding.addSequenceForStructFile(pdbFile, seq);
}
af.viewport.setColourAppliesToAllGroups(true);
- if (view.getShowSequenceFeatures())
- {
- af.viewport.showSequenceFeatures = true;
- }
+ af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
if (view.hasCentreColumnLabels())
{
af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.setFeaturesDisplayed(new Hashtable());
+ FeaturesDisplayed fdi;
+ af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
+ Hashtable featureGroups = new Hashtable();
+ Hashtable featureColours = new Hashtable();
+ Hashtable featureOrder = new Hashtable();
+
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), gc);
+ featureColours.put(setting.getType(), gc);
}
else
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
- setting.getType(),
+ featureColours.put(setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(), setting.getOrder());
+ featureOrder.put(setting.getType(), setting.getOrder());
}
else
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(),
- fs / jms.getFeatureSettings().getSettingCount());
+ featureOrder.put(setting.getType(), new Float(fs
+ / jms.getFeatureSettings().getSettingCount()));
}
if (setting.getDisplay())
{
- af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
- setting.getColour()));
+ fdi.setVisible(setting.getType());
}
}
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- Hashtable fgtable;
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ Hashtable fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
}
+ // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
+ // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, fgtable, featureColours, 1.0f, featureOrder);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
+
}
if (view.getHiddenColumnsCount() > 0)
{
skipList = skipList2;
}
-
}
git://source.jalview.org / jalview.git / blobdiff