<classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
<classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
<classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
+ <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
+ <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
++ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
label.search_filter = Search Filter
label.display_name = Display Label
label.description = Description
+label.include_description= Include Description
+
boolean hasHiddenRows();
/**
+ *
+ * @return a copy of this view's current display settings
+ */
+ public ViewStyleI getViewStyle();
+
+ /**
+ * update the view's display settings with the given style set
+ *
+ * @param settingsForView
+ */
+ public void setViewStyle(ViewStyleI settingsForView);
+
++ /**
+ * Returns a viewport which holds the cDna for this (protein), or vice versa,
+ * or null if none is set.
+ *
+ * @return
+ */
+ AlignViewportI getCodingComplement();
+
-
+ /**
+ * Sets the viewport which holds the cDna for this (protein), or vice versa.
+ * Implementation should guarantee that the reciprocal relationship is always
+ * set, i.e. each viewport is the complement of the other.
+ */
+ void setCodingComplement(AlignViewportI sl);
+
+ /**
+ * Answers true if viewport hosts DNA/RNA, else false.
+ *
+ * @return
+ */
+ boolean isNucleotide();
-
}
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
+import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
+ import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Color;
import java.awt.Container;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
+ import java.io.File;
+ import java.util.ArrayDeque;
import java.util.ArrayList;
+ import java.util.Deque;
import java.util.Hashtable;
- import java.util.Stack;
+ import java.util.Set;
import java.util.Vector;
+ import javax.swing.JInternalFrame;
+ import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
boolean gatherViewsHere = false;
- Stack<CommandI> historyList = new Stack<CommandI>();
+ private Deque<CommandI> historyList = new ArrayDeque<CommandI>();
- Stack<CommandI> redoList = new Stack<CommandI>();
+ private Deque<CommandI> redoList = new ArrayDeque<CommandI>();
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
-
private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
// TODO: verify that frames are recoverable when in headless mode
return null;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- ArrayList aps = new ArrayList();
- for (int t = 0; t < frames.length; t++)
+ List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>();
+ AlignFrame[] frames = getAlignFrames();
+ if (frames == null)
{
- if (frames[t] instanceof AlignFrame)
+ return null;
+ }
+ for (AlignFrame af : frames)
+ {
+ for (AlignmentPanel ap : af.alignPanels)
{
- AlignFrame af = (AlignFrame) frames[t];
- for (int a = 0; a < af.alignPanels.size(); a++)
- if (alignmentId.equals(ap.av.getSequenceSetId()))
++ if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId()))
{
- if (alignmentId == null
- || alignmentId.equals(((AlignmentPanel) af.alignPanels
- .elementAt(a)).av.getSequenceSetId()))
- {
- aps.add(af.alignPanels.elementAt(a));
- }
+ aps.add(ap);
}
}
+ // for (int a = 0; a < af.alignPanels.size(); a++)
+ // {
+ // if (alignmentId.equals(af.alignPanels
+ // .get(a).av.getSequenceSetId()))
+ // {
+ // aps.add(af.alignPanels.get(a));
+ // }
+ // }
}
if (aps.size() == 0)
{
* get all the viewports on an alignment.
*
* @param sequenceSetId
- * unique alignment id
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
* @return all viewports on the alignment bound to sequenceSetId
*/
- public static AlignViewport[] getViewports(String sequenceSetId)
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
{
- Vector viewp = new Vector();
+ List<AlignmentViewport> viewp = new ArrayList<AlignmentViewport>();
if (desktop != null)
{
- javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames();
- for (int t = 0; t < frames.length; t++)
+ for (AlignFrame afr : frames)
{
- if (frames[t] instanceof AlignFrame)
- if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
++ if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId))
{
- AlignFrame afr = ((AlignFrame) frames[t]);
- if (sequenceSetId == null
- || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
+ if (afr.alignPanels != null)
{
- if (afr.alignPanels != null)
+ for (AlignmentPanel ap : afr.alignPanels)
{
- for (int a = 0; a < afr.alignPanels.size(); a++)
- if (sequenceSetId.equals(ap.av.getSequenceSetId()))
++ if (sequenceSetId == null
++ || sequenceSetId.equals(ap.av.getSequenceSetId()))
{
- if (sequenceSetId == null
- || sequenceSetId
- .equals(((AlignmentPanel) afr.alignPanels
- .elementAt(a)).av.getSequenceSetId()))
- {
- viewp.addElement(((AlignmentPanel) afr.alignPanels
- .elementAt(a)).av);
- }
+ viewp.add(ap.av);
}
}
- else
- {
- viewp.addElement(((AlignFrame) frames[t]).getViewport());
- }
+ }
+ else
+ {
+ viewp.add(afr.getViewport());
}
}
}
{
string = String.valueOf(av.getColumnSelection()
.adjustForHiddenColumns(i));
- if ((i - startx - 1) * av.charWidth > maxX)
+ if ((i - startx - 1) * avCharWidth > maxX)
{
- gg.drawString(string, (i - startx - 1) * av.charWidth, y);
- maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+ gg.drawString(string, (i - startx - 1) * avCharWidth, y);
+ maxX = (i - startx + 1) * avCharWidth + fm.stringWidth(string);
}
- gg.drawLine(
- ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
- gg.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- y + 2, ((i - startx - 1) * av.charWidth)
- + (av.charWidth / 2), y + (fm.getDescent() * 2));
-
++ gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
+ y + 2,
+ ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
+ y + (fm.getDescent() * 2));
}
else
{
- gg.drawLine(
- ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
- y + fm.getDescent(),
- ((i - startx - 1) * avCharWidth)
- + (avCharWidth / 2),
- y + (fm.getDescent() * 2));
- gg.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- y + fm.getDescent(), ((i - startx - 1) * av.charWidth)
- + (av.charWidth / 2), y + (fm.getDescent() * 2));
++ gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
++ y + fm.getDescent(), ((i - startx - 1) * avCharWidth)
++ + (avCharWidth / 2), y + (fm.getDescent() * 2));
}
}
* @author jimp
*
*/
-public abstract class AlignmentViewport implements AlignViewportI
+public abstract class AlignmentViewport implements AlignViewportI,
+ ViewStyleI
{
- /*
+ protected ViewStyleI viewStyle = new ViewStyle();
-
-
++
++ /**
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
+ */
+ AlignViewportI codingComplement = null;
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * @param name
+ * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
- protected AlignmentI alignment;
+ public void setFontName(String name)
+ {
+ viewStyle.setFontName(name);
+ }
- protected String sequenceSetID;
+ /**
+ * @param style
+ * @see jalview.api.ViewStyleI#setFontStyle(int)
+ */
+ public void setFontStyle(int style)
+ {
+ viewStyle.setFontStyle(style);
+ }
/**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
+ * @param size
+ * @see jalview.api.ViewStyleI#setFontSize(int)
*/
- protected boolean isDataset = false;
+ public void setFontSize(int size)
+ {
+ viewStyle.setFontSize(size);
+ }
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontStyle()
+ */
+ public int getFontStyle()
+ {
+ return viewStyle.getFontStyle();
+ }
- protected ColumnSelection colSel = new ColumnSelection();
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontName()
+ */
+ public String getFontName()
+ {
+ return viewStyle.getFontName();
+ }
- public boolean autoCalculateConsensus = true;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontSize()
+ */
+ public int getFontSize()
+ {
+ return viewStyle.getFontSize();
+ }
- protected boolean autoCalculateStrucConsensus = true;
+ /**
+ * @param upperCasebold
+ * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
+ */
+ public void setUpperCasebold(boolean upperCasebold)
+ {
+ viewStyle.setUpperCasebold(upperCasebold);
+ }
- protected boolean ignoreGapsInConsensusCalculation = false;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isUpperCasebold()
+ */
+ public boolean isUpperCasebold()
+ {
+ return viewStyle.isUpperCasebold();
+ }
- protected ColourSchemeI globalColourScheme = null;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isSeqNameItalics()
+ */
+ public boolean isSeqNameItalics()
+ {
+ return viewStyle.isSeqNameItalics();
+ }
/**
- * gui state - changes to colour scheme propagated to all groups
+ * @param colourByReferenceSeq
+ * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
*/
- private boolean colourAppliesToAllGroups;
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
+ }
/**
- * @param value
- * indicating if subsequent colourscheme changes will be propagated
- * to all groups
+ * @param b
+ * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
*/
public void setColourAppliesToAllGroups(boolean b)
{
@Override
public void setDisplayReferenceSeq(boolean displayReferenceSeq)
{
- this.displayReferenceSeq = displayReferenceSeq;
+ viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
}
+ @Override
public boolean isColourByReferenceSeq()
{
- return alignment.hasSeqrep() && colourByReferenceSeq;
- }
-
- @Override
- public void setColourByReferenceSeq(boolean colourByReferenceSeq)
- {
- this.colourByReferenceSeq = colourByReferenceSeq;
+ return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
}
-
@Override
public Color getSequenceColour(SequenceI seq)
{
@Override
public void setRightAlignIds(boolean rightAlignIds)
{
- this.rightAlignIds = rightAlignIds;
+ viewStyle.setRightAlignIds(rightAlignIds);
+ }
+
+ @Override
+ public boolean getConservationSelected()
+ {
+ return viewStyle.getConservationSelected();
+ }
+
+ @Override
+ public void setShowBoxes(boolean state)
+ {
+ viewStyle.setShowBoxes(state);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour()
+ */
+ public Color getTextColour()
+ {
+ return viewStyle.getTextColour();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour2()
+ */
+ public Color getTextColour2()
+ {
+ return viewStyle.getTextColour2();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getThresholdTextColour()
+ */
+ public int getThresholdTextColour()
+ {
+ return viewStyle.getThresholdTextColour();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isConservationColourSelected()
+ */
+ public boolean isConservationColourSelected()
+ {
+ return viewStyle.isConservationColourSelected();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isRenderGaps()
+ */
+ public boolean isRenderGaps()
+ {
+ return viewStyle.isRenderGaps();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowColourText()
+ */
+ public boolean isShowColourText()
+ {
+ return viewStyle.isShowColourText();
+ }
-
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
+ */
+ public boolean isShowSeqFeaturesHeight()
+ {
+ return viewStyle.isShowSeqFeaturesHeight();
+ }
+
+ /**
+ * @param conservationColourSelected
+ * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
+ */
+ public void setConservationColourSelected(
+ boolean conservationColourSelected)
+ {
+ viewStyle.setConservationColourSelected(conservationColourSelected);
+ }
+
+ /**
+ * @param showColourText
+ * @see jalview.api.ViewStyleI#setShowColourText(boolean)
+ */
+ public void setShowColourText(boolean showColourText)
+ {
+ viewStyle.setShowColourText(showColourText);
+ }
+
+ /**
+ * @param textColour
+ * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
+ */
+ public void setTextColour(Color textColour)
+ {
+ viewStyle.setTextColour(textColour);
+ }
+
+ /**
+ * @param thresholdTextColour
+ * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
+ */
+ public void setThresholdTextColour(int thresholdTextColour)
+ {
+ viewStyle.setThresholdTextColour(thresholdTextColour);
+ }
+
+ /**
+ * @param textColour2
+ * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
+ */
+ public void setTextColour2(Color textColour2)
+ {
+ viewStyle.setTextColour2(textColour2);
+ }
+
+ @Override
+ public ViewStyleI getViewStyle()
+ {
+ return new ViewStyle(viewStyle);
+ }
+
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ viewStyle = new ViewStyle(settingsForView);
+ }
+
+ @Override
+ public boolean sameStyle(ViewStyleI them)
+ {
+ return viewStyle.sameStyle(them);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIdWidth()
+ */
+ public int getIdWidth()
+ {
+ return viewStyle.getIdWidth();
+ }
+
+ /**
+ * @param i
+ * @see jalview.api.ViewStyleI#setIdWidth(int)
+ */
+ public void setIdWidth(int i)
+ {
+ viewStyle.setIdWidth(i);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isCentreColumnLabels()
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return viewStyle.isCentreColumnLabels();
+ }
+
+ /**
+ * @param centreColumnLabels
+ * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
+ */
+ public void setCentreColumnLabels(boolean centreColumnLabels)
+ {
+ viewStyle.setCentreColumnLabels(centreColumnLabels);
+ }
+
+ /**
+ * @param showdbrefs
+ * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
+ */
+ public void setShowDBRefs(boolean showdbrefs)
+ {
+ viewStyle.setShowDBRefs(showdbrefs);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowDBRefs()
+ */
+ public boolean isShowDBRefs()
+ {
+ return viewStyle.isShowDBRefs();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowNPFeats()
+ */
+ public boolean isShowNPFeats()
+ {
+ return viewStyle.isShowNPFeats();
+ }
+
+ /**
+ * @param shownpfeats
+ * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
+ */
+ public void setShowNPFeats(boolean shownpfeats)
+ {
+ viewStyle.setShowNPFeats(shownpfeats);
}
}
git://source.jalview.org / jalview.git / commitdiff