*/
package jalview.api;
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import jalview.viewmodel.seqfeatures.IdColumns;
/**
* @author jimp
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+ IdColumns getIdColumns();
+
ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}
import jalview.datamodel.SequenceI;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.IdColumn;
+import jalview.viewmodel.seqfeatures.IdColumns;
+import jalview.viewmodel.seqfeatures.IdColumns.ColumnCell;
/**
* DOCUMENT ME!
}
// Now draw the id strings
- int panelWidth = getWidth();
- int xPos = 0;
+ int fullPanelWidth = getWidth();
+
+ IdColumns id_cols = alignViewport.getIdColumns();
+ List<IdColumn> visible = id_cols.getVisible();
+ /**
+ * width of an idColumn
+ */
+ int colWid = 20;
+ int panelWidth = Math.max(fullPanelWidth / 2,
+ fullPanelWidth - (colWid * visible.size()));
// Now draw the id strings
for (int i = startSeq; i <= endSeq; i++)
{
+ int xPos = 0;
SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
if (sequence == null)
{
continue;
}
-
if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
{
g.setFont(getHiddenFont(sequence, alignViewport));
(((i - startSeq) * charHeight) + charHeight)
- (charHeight / 5));
+ if (visible != null && visible.size() > 0)
+ {
+ try
+ {
+ xPos = panelWidth + 2;
+ for (IdColumn col : visible)
+ {
+ ColumnCell col_cell = id_cols.getCellFor(sequence, col);
+ if (col_cell == null)
+ {
+ g.setColor(Color.gray);
+ g.fillRect(xPos + 1, (i - startSeq) * charHeight,
+ xPos + colWid - 3, charHeight);
+ }
+ else
+ {
+ g.setColor(col_cell.bg);
+ g.fillRect(xPos + 1, (i - startSeq) * charHeight,
+ xPos + colWid - 3, charHeight);
+ g.setColor(col_cell.fg);
+ g.drawString(col_cell.label, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
+ }
+ xPos += colWid;
+ g.setColor(currentTextColor);
+ }
+ } catch (Exception q)
+ {
+ }
+ }
if (hasHiddenRows && av.getShowHiddenMarkers())
{
drawMarker(g, alignViewport, i, startSeq, 0);
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.IdColumn;
+import jalview.viewmodel.seqfeatures.IdColumns;
+import jalview.viewmodel.seqfeatures.IdColumns.ColumnCell;
/**
* This panel hosts alignment sequence ids and responds to mouse clicks on them,
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
StringBuilder tip = new StringBuilder(64);
tip.append(sequence.getDisplayId(true)).append(" ");
- seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
- av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
+ IdColumn col = locateColumnFor(e);
+ if (col != null)
+ {
+ // tooltip for column
+ tip.append(getTooltipFor(col, sequence));
+ }
+ else
+ {
+ seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
+ }
setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
StringBuilder text = new StringBuilder();
}
}
+ private Object getTooltipFor(IdColumn col, SequenceI seq)
+ {
+ ColumnCell cell = av.getIdColumns().getCellFor(seq, col);
+ if (cell != null)
+ {
+ return "" + col.getLabel() + ": " + cell.label;
+ }
+ return "";
+ }
+
+ private IdColumn locateColumnFor(MouseEvent e)
+ {
+ // TODO COMBINE SAME CODE IN IDCANVAS!!!
+
+ IdColumns id_cols = av.getIdColumns();
+ List<IdColumn> visible = id_cols.getVisible();
+ /**
+ * width of an idColumn
+ */
+ int colWid = 20;
+ int panelWidth = Math.max(idCanvas.getWidth() / 2,
+ idCanvas.getWidth() - (colWid * visible.size()));
+ int p = 0;
+ while (panelWidth < idCanvas.getWidth() && p < visible.size())
+ {
+
+ if (e.getX() >= panelWidth && e.getX() < panelWidth + colWid)
+ return visible.get(p);
+ p++;
+ panelWidth += colWid;
+ }
+ return null;
+ }
+
/**
* Responds to a mouse drag by selecting the sequences under the dragged
* region.
import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.viewmodel.seqfeatures.IdColumn;
+import jalview.viewmodel.seqfeatures.IdColumns;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
rnaStructureMenu.setVisible(false);
}
+ if (forIdPanel)
+ {
+ addDisplayColumnsMenu();
+ }
+
addLinksAndFeatures(seq, column);
}
+ void addDisplayColumnsMenu()
+ {
+ JMenu dis_cols = new JMenu(
+ MessageManager.getString("action.displayed_columns"));
+ final IdColumns id_cols = ap.av.getIdColumns();
+ id_cols.updateTypeList();
+ for (final IdColumn col : id_cols.getIdColumns())
+ {
+ JMenuItem col_entry = new JCheckBoxMenuItem(col.getLabel(),
+ col.isVisible());
+ col_entry.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ id_cols.toggleVisible(col.getLabel());
+ }
+ });
+ dis_cols.add(col_entry);
+ }
+ add(dis_cols);
+ }
+
/**
* Adds
* <ul>
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.IdColumns;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
false));
}
+ /**
+ * ordered list of annotation values displayed per sequence in ID panel
+ */
+ private IdColumns id_columns = null;
+
+ /**
+ * available and currently visible columns for this view
+ */
+ @Override
+ public IdColumns getIdColumns()
+ {
+ if (alignment == null)
+ {
+ return null;
+ }
+ if (id_columns == null)
+ {
+ id_columns = new IdColumns(alignment);
+ }
+ return id_columns;
+ }
+
public void setSavedUpToDate(boolean s)
{
setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
--- /dev/null
+package jalview.viewmodel.seqfeatures;
+
+public class IdColumn
+{
+ String name;
+
+ String descr;
+
+ boolean visible;
+
+ /**
+ * name of the feature this column shows
+ */
+ String featureTypeName = null;
+
+ /**
+ * group to select feature(s)
+ */
+ String featureGroupName = null;
+
+ /**
+ * Label string for annotation row
+ */
+ String annotationTypeName = null;
+
+ /**
+ * calcId for annotation row
+ */
+ String annotationTypeCalcId = null;
+
+ public String DbRefName = null;
+
+ public IdColumn(String string, String description, boolean b)
+ {
+ name = string;
+ descr = description;
+ visible = b;
+ }
+
+ public String getLabel()
+ {
+ return name;
+ }
+
+ public boolean isVisible()
+ {
+ return visible;
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.viewmodel.seqfeatures;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.api.DBRefEntryI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+
+public class IdColumns
+{
+
+ AlignmentI alignment = null;
+
+ public IdColumns(AlignmentI al)
+ {
+ alignment = al;
+ columns.put(STRUCTURES_NUM.getLabel(), STRUCTURES_NUM);
+ updateTypeList();
+ }
+
+ public final static IdColumn STRUCTURES_NUM;
+ static
+ {
+ STRUCTURES_NUM = new IdColumn("3D Structures",
+ "Number of associated structure files", false);
+ }
+
+ LinkedHashMap<String, IdColumn> columns = new LinkedHashMap<String, IdColumn>();
+
+ /**
+ * register a feature on the columnset
+ *
+ * @param sf
+ * @return true if feature was not seen before
+ */
+ boolean updateListForFeature(SequenceFeature sf)
+ {
+ String colname = sf.getType();
+ if (columns.get(colname) != null)
+ {
+ return false;
+ }
+
+ IdColumn col = new IdColumn(colname,
+ "Nonpositional feature: " + colname, false);
+ col.featureTypeName = sf.getType();
+ // col.featureGroupName = sf.getFeatureGroup();
+ columns.put(colname, col);
+ return true;
+ }
+
+ boolean updateListForDbxref(DBRefEntryI dbref)
+ {
+ String colname = dbref.getSource();
+ if (columns.get(colname) != null)
+ {
+ return false;
+ }
+
+ IdColumn col = new IdColumn(colname,
+ "Database CrossReference: " + colname, false);
+ col.DbRefName = colname;
+ // col.featureGroupName = sf.getFeatureGroup();
+ columns.put(colname, col);
+ return true;
+ }
+
+ public void updateTypeList()
+ {
+ for (SequenceI sq : alignment.getSequences())
+ {
+ SequenceI seq = sq;
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ SequenceFeaturesI sqf = seq.getFeatures();
+ List<SequenceFeature> nonpos = sqf.getNonPositionalFeatures();
+ if (nonpos != null)
+ {
+ for (SequenceFeature sf : nonpos)
+ {
+ updateListForFeature(sf);
+ }
+ }
+ if (seq.getDBRefs() != null)
+ {
+ for (DBRefEntryI dbr : seq.getDBRefs())
+ {
+ updateListForDbxref(dbr);
+ }
+ }
+ }
+ }
+
+ public void toggleVisible(String column)
+ {
+ IdColumn col = columns.get(column);
+ if (col != null)
+ {
+ col.visible = !col.visible;
+ }
+ }
+
+ public List<IdColumn> getVisible()
+ {
+ // probably want to cache this
+ ArrayList<IdColumn> vis = new ArrayList();
+ for (IdColumn col : columns.values())
+ {
+ if (col.visible)
+ {
+ vis.add(col);
+ }
+ }
+ return vis;
+ }
+
+ public final class ColumnCell
+ {
+ public final String label;
+
+ public final Color bg;
+
+ public final Color fg;
+
+ public ColumnCell(final String label, final Color bg, final Color fg)
+ {
+ this.label = label;
+ this.bg = bg;
+ this.fg = fg;
+ }
+ }
+
+ /**
+ * render the column value for this sequence
+ *
+ * @param seq
+ * @param col
+ * @return
+ */
+ public ColumnCell getCellFor(SequenceI seq, IdColumn col)
+ {
+ ColumnCell cell = null;
+ if (col != null)
+ {
+ SequenceI dseq = seq;
+ while (dseq.getDatasetSequence() != null)
+ {
+ dseq = dseq.getDatasetSequence();
+ }
+ if (col == STRUCTURES_NUM)
+ {
+ Vector pdbE = dseq.getAllPDBEntries();
+ if (pdbE == null)
+ {
+ return null;
+ }
+ return new ColumnCell("" + pdbE.size(), Color.red, Color.white);
+ }
+ if (col.featureTypeName != null)
+ {
+ List<SequenceFeature> np = dseq.getFeatures()
+ .getNonPositionalFeatures(col.featureTypeName);
+ if (np != null)
+ {
+ for (SequenceFeature npfeat : np)
+ {
+ // nb deal with multiplicities!
+ if (col.featureGroupName == null || (npfeat.featureGroup != null
+ && npfeat.featureGroup.equals(col.featureGroupName)))
+ {
+ Color fg = Color.black;
+ Color bg = Color.white;
+
+ return new ColumnCell(npfeat.description, fg, bg);
+ }
+ }
+ }
+ }
+ if (col.DbRefName != null)
+ {
+ List<DBRefEntryI> refs = new ArrayList<DBRefEntryI>();
+ for (DBRefEntryI dbr : dseq.getDBRefs())
+ {
+ if (dbr.getSource().equals(col.DbRefName))
+ {
+ refs.add(dbr);
+ }
+ }
+ if (refs.size()==0)
+ {
+ return null;
+ }
+ StringBuilder dbr = new StringBuilder();
+ dbr.append(refs.size());
+ for (DBRefEntryI ref : refs)
+ {
+ dbr.append(" "+ref.getAccessionId());
+ }
+ return new ColumnCell(dbr.toString(), Color.black, Color.white);
+
+ }
+ }
+ // no value for this sequence in given column
+ return null;
+ }
+
+ public IdColumn[] getIdColumns()
+ {
+ return columns.values().toArray(new IdColumn[0]);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff