*/
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
*/
SearchResultsI getSearchResults();
+ /**
+ * Retrieve a ContactListI corresponding to column in an annotation row in an
+ * alignment.
+ *
+ * @param _aa
+ * - annotation with associated matrix data
+ * @param column
+ * - column in alignment where _aa is associated
+ */
ContactListI getContactList(AlignmentAnnotation _aa, int column);
/**
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+ IdColumns getIdColumns();
+
ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}
import java.awt.BorderLayout;
import java.awt.Color;
+ import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
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!
gg.translate(0, transY);
- drawIds(gg, av, ss, es, searchResults);
+ drawIds(gg, av, ss, es, searchResults,true);
gg.translate(0, -transY);
gg.fillRect(0, 0, getWidth(), imgHeight);
drawIds(gg, av, av.getRanges().getStartSeq(),
- av.getRanges().getEndSeq(), searchResults);
+ av.getRanges().getEndSeq(), searchResults,true);
gg.dispose();
* @param selection
*/
void drawIds(Graphics2D g, AlignViewport alignViewport,
- final int startSeq, final int endSeq, List<SequenceI> selection)
+ final int startSeq, final int endSeq, List<SequenceI> selection, boolean forGUI)
{
Font font = alignViewport.getFont();
if (alignViewport.isSeqNameItalics())
}
// 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);
void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
int startSeq, int pageHeight)
{
+ drawIdsWrapped(g, alignViewport, startSeq, pageHeight, -1, true);
+ }
+
+ /**
+ * render sequence IDs and annotation labels when wrapped - without GUI junk
+ * @param g
+ * @param av2
+ * @param i
+ * @param totalHeight
+ */
+ public void drawIdsWrappedNoGUI(Graphics2D g, AlignViewport av2, int i,
+ int totalHeight)
+ {
+ drawIdsWrapped(g, av2, totalHeight, totalHeight, i,false);
+ }
+
+ void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+ int startSeq, int pageHeight, int idWidth, boolean forGUI)
+ {
int alignmentWidth = alignViewport.getAlignment().getWidth();
final int alheight = alignViewport.getAlignment().getHeight();
if (labels != null && alignViewport.isShowAnnotation())
{
+ int getWidth = getWidth();
+ int thisIdWidth = getWidth;
g.translate(0, ypos + (alheight * charHeight));
- labels.drawComponent(g, getWidth());
+ if (!manuallyAdjusted())
+ {
+ int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,forGUI,
+ null);
+ thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth;
+ if (thisIdWidth > getWidth)
+ {
+ this.setPreferredSize(
+ new Dimension(thisIdWidth, this.getHeight()));
+ this.repaint();
+ alignViewport.setIdWidth(thisIdWidth);
+ }
+ }
+ labels.drawComponent(g, false, thisIdWidth, forGUI);
g.translate(0, -ypos - (alheight * charHeight));
}
repaint();
}
}
+
+ private boolean manuallyAdjusted = false;
+
+ public boolean manuallyAdjusted()
+ {
+ return manuallyAdjusted;
+ }
+
+ public void setManuallyAdjusted(boolean b)
+ {
+ manuallyAdjusted = b;
+ }
+
}
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>
if (Platform.isJS())
{
details = new JInternalFrame();
+ details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
panel.setBackground(Color.white);
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ null);
refresh();
}
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
else
sg.setName(dialog.getName());
sg.setDescription(dialog.getDescription());
refresh();
- return null;
});
}
{
if (dialog.getName().indexOf(" ") > -1)
{
- JvOptionPane.showMessageDialog(ap,
- MessageManager.getString(
- "label.spaces_converted_to_underscores"),
- MessageManager.getString(
- "label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
+ String ok = MessageManager.getString("action.ok");
+ String cancel = MessageManager.getString("action.cancel");
+ String message = MessageManager.getString(
+ "label.spaces_converted_to_underscores");
+ String title = MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name");
+ Object[] options = new Object[] { ok, cancel };
+
+ JvOptionPane.frameDialog(message, title,
+ JvOptionPane.WARNING_MESSAGE, null, null, null,
+ false);
}
sequence.setName(dialog.getName().replace(' ', '_'));
ap.paintAlignment(false, false);
sequence.setDescription(dialog.getDescription());
ap.av.firePropertyChange("alignment", null,
ap.av.getAlignment().getSequences());
- return null;
});
}
String[] omitHidden = null;
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
ap.alignFrame.addHistoryItem(editCommand);
ap.av.firePropertyChange("alignment", null,
ap.av.getAlignment().getSequences());
- return null;
});
}
}
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;
}
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
- // System.err.println("grey out ("+alignmentAnnotation.label+")");
+ // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
return true;
}
return false;
{
if (sequenceSetID != null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning - overwriting a sequenceSetId for a viewport!");
}
sequenceSetID = new String(newid);
{
if (aa == null)
{
- System.err.println("Null annotation row: ignoring.");
+ jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
continue;
}
if (!aa.visible)
if (aa.graph > 0)
{
- aa.height += aa.graphHeight;
+ aa.height += aa.graphHeight+20;
}
if (aa.height == 0)
{
if (this == av)
{
- System.err.println("Ignoring recursive setCodingComplement request");
+ jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
}
else
{
return alignment.getContactMatrixFor(alignmentAnnotation);
}
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
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);
git://source.jalview.org / jalview.git / commitdiff