--- /dev/null
+package jalview.api;
+
+import java.awt.Color;
+
+public interface ViewStyleI
+{
+
+ void setColourAppliesToAllGroups(boolean b);
+
+ boolean getColourAppliesToAllGroups();
+
+ boolean getAbovePIDThreshold();
+
+ void setIncrement(int inc);
+
+ int getIncrement();
+
+ boolean getConservationSelected();
+
+ void setConservationSelected(boolean b);
+
+ void setShowHiddenMarkers(boolean show);
+
+ boolean getShowHiddenMarkers();
+
+ void setScaleRightWrapped(boolean b);
+
+ void setScaleLeftWrapped(boolean b);
+
+ void setScaleAboveWrapped(boolean b);
+
+ boolean getScaleLeftWrapped();
+
+ boolean getScaleAboveWrapped();
+
+ boolean getScaleRightWrapped();
+
+ void setAbovePIDThreshold(boolean b);
+
+ void setThreshold(int thresh);
+
+ int getThreshold();
+
+ boolean getShowJVSuffix();
+
+ void setShowJVSuffix(boolean b);
+
+ void setWrapAlignment(boolean state);
+
+ void setShowText(boolean state);
+
+ void setRenderGaps(boolean state);
+
+ boolean getColourText();
+
+ void setColourText(boolean state);
+
+ void setShowBoxes(boolean state);
+
+ boolean getWrapAlignment();
+
+ boolean getShowText();
+
+ int getWrappedWidth();
+
+ void setWrappedWidth(int w);
+
+ int getCharHeight();
+
+ void setCharHeight(int h);
+
+ int getCharWidth();
+
+ void setCharWidth(int w);
+
+ boolean getShowBoxes();
+
+ boolean getShowUnconserved();
+
+ void setShowUnconserved(boolean showunconserved);
+
+ boolean isDisplayReferenceSeq();
+
+ void setDisplayReferenceSeq(boolean displayReferenceSeq);
+
+ boolean isColourByReferenceSeq();
+
+ void setSeqNameItalics(boolean default1);
+
+ void setShowSequenceFeatures(boolean b);
+
+ boolean isShowSequenceFeatures();
+
+ boolean isRightAlignIds();
+
+ void setRightAlignIds(boolean rightAlignIds);
+
+ boolean isShowAnnotation();
+
+ void setShowAnnotation(boolean b);
+
+ void setShowSeqFeaturesHeight(boolean selected);
+
+ boolean isShowSequenceFeaturesHeight();
+
+ void setColourByReferenceSeq(boolean colourByReferenceSeq);
+
+ Color getTextColour();
+
+ Color getTextColour2();
+
+ int getThresholdTextColour();
+
+ boolean isConservationColourSelected();
+
+ boolean isRenderGaps();
+
+ boolean isShowColourText();
+
+ boolean isShowSeqFeaturesHeight();
+
+ void setConservationColourSelected(boolean conservationColourSelected);
+
+ void setShowColourText(boolean showColourText);
+
+ void setTextColour(Color textColour);
+
+ void setThresholdTextColour(int thresholdTextColour);
+
+ void setTextColour2(Color textColour2);
+
+ boolean isSeqNameItalics();
+
+ void setUpperCasebold(boolean upperCasebold);
+
+ boolean isUpperCasebold();
+
+}
boolean cursorMode = false;
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- boolean showAnnotation = true;
-
- boolean upperCasebold = false;
-
- int charHeight;
-
- int charWidth;
-
- int wrappedWidth;
-
Font font = new Font("SansSerif", Font.PLAIN, 10);
boolean validCharWidth = true;
- int threshold;
-
- int increment;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = true;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
public jalview.bin.JalviewLite applet;
boolean MAC = false;
public AlignViewport(AlignmentI al, JalviewLite applet)
{
+ super();
calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
- setAlignment(al);
+ alignment = al;
// we always pad gaps
this.setPadGaps(true);
this.startRes = 0;
if (applet != null)
{
- showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+ setShowJVSuffix(applet.getDefaultParameter("showFullId",
+ getShowJVSuffix()));
- showAnnotation = applet.getDefaultParameter("showAnnotation",
- showAnnotation);
+ setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+ isShowAnnotation()));
showConservation = applet.getDefaultParameter("showConservation",
showConservation);
showConsensus = applet.getDefaultParameter("showConsensus",
showConsensus);
- showUnconserved = applet.getDefaultParameter("showUnconserved",
- showUnconserved);
+ setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+ getShowUnconserved()));
String param = applet.getParameter("upperCase");
if (param != null)
{
if (param.equalsIgnoreCase("bold"))
{
- upperCasebold = true;
+ setUpperCasebold(true);
}
}
sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
setCharHeight((int) (heightScale * fm.getHeight()));
- charWidth = (int) (widthScale * fm.charWidth('M'));
+ setCharWidth((int) (widthScale * fm.charWidth('M')));
- if (upperCasebold)
+ if (isUpperCasebold())
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+ setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
return font;
}
- public int getCharWidth()
- {
- return charWidth;
- }
-
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- public int getCharHeight()
- {
- return charHeight;
- }
-
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- public int getwrappedWidth()
- {
- return wrappedWidth;
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI align)
- {
- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- public boolean getShowText()
- {
- return showText;
- }
-
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
public void resetSeqLimits(int height)
{
return currentTree;
}
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(null);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
- }
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
boolean centreColumnLabels;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Color;
import java.awt.Container;
import java.awt.Font;
import java.awt.Rectangle;
int endSeq;
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
SequenceAnnotationOrder sortAnnotationsBy = null;
- int charHeight;
-
- int charWidth;
-
- boolean validCharWidth;
-
- int wrappedWidth;
-
Font font;
- boolean seqNameItalics;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
boolean cursorMode = false;
boolean antiAlias = false;
Stack<CommandI> redoList = new Stack<CommandI>();
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
-
private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
init();
}
- void init()
+ private void applyViewProperties()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
-
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
setPadGaps(Cache.getDefault("PAD_GAPS", true));
shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(Cache
+ .getDefault("SHOW_UNCONSERVED", false));
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
int style = 0;
if (fontStyle.equals("bold"))
globalColourScheme.setConsensus(hconsensus);
}
}
-
- wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
- sortByTree = Cache.getDefault("SORT_BY_TREE", false);
- followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**
return endSeq;
}
+ boolean validCharWidth;
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param w
- * DOCUMENT ME!
- */
- public void setCharWidth(int w)
- {
- this.charWidth = w;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharWidth()
- {
- return charWidth;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param h
- * DOCUMENT ME!
- */
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
- {
- return charHeight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
- */
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
- {
- return wrappedWidth;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param align
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*
- * @param state
- * DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return showColourText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
+import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
* @author jimp
*
*/
-public abstract class AlignmentViewport implements AlignViewportI
+public abstract class AlignmentViewport implements AlignViewportI,
+ ViewStyleI
{
+ protected ViewStyleI viewStyle = new ViewStyle();
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * @param upperCasebold
+ * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
*/
- protected AlignmentI alignment;
+ public void setUpperCasebold(boolean upperCasebold)
+ {
+ viewStyle.setUpperCasebold(upperCasebold);
+ }
- protected String sequenceSetID;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isUpperCasebold()
+ */
+ public boolean isUpperCasebold()
+ {
+ return viewStyle.isUpperCasebold();
+ }
/**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
+ * @return
+ * @see jalview.api.ViewStyleI#isSeqNameItalics()
*/
- protected boolean isDataset = false;
+ public boolean isSeqNameItalics()
+ {
+ return viewStyle.isSeqNameItalics();
+ }
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+ /**
+ * @param colourByReferenceSeq
+ * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
+ */
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
+ }
- protected ColumnSelection colSel = new ColumnSelection();
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ viewStyle.setColourAppliesToAllGroups(b);
+ }
- public boolean autoCalculateConsensus = true;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return viewStyle.getColourAppliesToAllGroups();
+ }
- protected boolean autoCalculateStrucConsensus = true;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return viewStyle.getAbovePIDThreshold();
+ }
- protected boolean ignoreGapsInConsensusCalculation = false;
+ /**
+ * @param inc
+ * @see jalview.api.ViewStyleI#setIncrement(int)
+ */
+ public void setIncrement(int inc)
+ {
+ viewStyle.setIncrement(inc);
+ }
- protected ColourSchemeI globalColourScheme = null;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIncrement()
+ */
+ public int getIncrement()
+ {
+ return viewStyle.getIncrement();
+ }
/**
- * gui state - changes to colour scheme propagated to all groups
+ * @param b
+ * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
*/
- private boolean colourAppliesToAllGroups;
+ public void setConservationSelected(boolean b)
+ {
+ viewStyle.setConservationSelected(b);
+ }
/**
- * @param value
- * indicating if subsequent colourscheme changes will be propagated
- * to all groups
+ * @param show
+ * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
*/
- public void setColourAppliesToAllGroups(boolean b)
+ public void setShowHiddenMarkers(boolean show)
{
- colourAppliesToAllGroups = b;
+ viewStyle.setShowHiddenMarkers(show);
}
/**
- *
- *
- * @return flag indicating if colourchanges propagated to all groups
+ * @return
+ * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
*/
- public boolean getColourAppliesToAllGroups()
+ public boolean getShowHiddenMarkers()
{
- return colourAppliesToAllGroups;
+ return viewStyle.getShowHiddenMarkers();
}
- boolean abovePIDThreshold = false;
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ viewStyle.setScaleRightWrapped(b);
+ }
/**
- * GUI state
- *
- * @return true if percent identity threshold is applied to shading
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
*/
- public boolean getAbovePIDThreshold()
+ public void setScaleLeftWrapped(boolean b)
{
- return abovePIDThreshold;
+ viewStyle.setScaleLeftWrapped(b);
}
/**
- * GUI state
- *
- *
* @param b
- * indicate if percent identity threshold is applied to shading
+ * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
*/
- public void setAbovePIDThreshold(boolean b)
+ public void setScaleAboveWrapped(boolean b)
{
- abovePIDThreshold = b;
+ viewStyle.setScaleAboveWrapped(b);
}
- int threshold;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return viewStyle.getScaleLeftWrapped();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return viewStyle.getScaleAboveWrapped();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleRightWrapped()
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return viewStyle.getScaleRightWrapped();
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ viewStyle.setAbovePIDThreshold(b);
+ }
/**
- * DOCUMENT ME!
- *
* @param thresh
- * DOCUMENT ME!
+ * @see jalview.api.ViewStyleI#setThreshold(int)
*/
public void setThreshold(int thresh)
{
- threshold = thresh;
+ viewStyle.setThreshold(thresh);
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return
+ * @see jalview.api.ViewStyleI#getThreshold()
*/
public int getThreshold()
{
- return threshold;
+ return viewStyle.getThreshold();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowJVSuffix()
+ */
+ public boolean getShowJVSuffix()
+ {
+ return viewStyle.getShowJVSuffix();
}
- int increment;
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
+ */
+ public void setShowJVSuffix(boolean b)
+ {
+ viewStyle.setShowJVSuffix(b);
+ }
/**
- *
- * @param inc
- * set the scalar for bleaching colourschemes according to degree of
- * conservation
+ * @param state
+ * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
*/
- public void setIncrement(int inc)
+ public void setWrapAlignment(boolean state)
{
- increment = inc;
+ viewStyle.setWrapAlignment(state);
}
/**
- * GUI State
- *
- * @return get scalar for bleaching colourschemes by conservation
+ * @param state
+ * @see jalview.api.ViewStyleI#setShowText(boolean)
*/
- public int getIncrement()
+ public void setShowText(boolean state)
{
- return increment;
+ viewStyle.setShowText(state);
}
- boolean conservationColourSelected = false;
+ /**
+ * @param state
+ * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
+ */
+ public void setRenderGaps(boolean state)
+ {
+ viewStyle.setRenderGaps(state);
+ }
/**
- * GUI state
- *
- * @return true if conservation based shading is enabled
+ * @return
+ * @see jalview.api.ViewStyleI#getColourText()
*/
- public boolean getConservationSelected()
+ public boolean getColourText()
{
- return conservationColourSelected;
+ return viewStyle.getColourText();
}
/**
- * GUI state
- *
- * @param b
- * enable conservation based shading
+ * @param state
+ * @see jalview.api.ViewStyleI#setColourText(boolean)
*/
- public void setConservationSelected(boolean b)
+ public void setColourText(boolean state)
{
- conservationColourSelected = b;
+ viewStyle.setColourText(state);
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getWrapAlignment()
+ */
+ public boolean getWrapAlignment()
+ {
+ return viewStyle.getWrapAlignment();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowText()
+ */
+ public boolean getShowText()
+ {
+ return viewStyle.getShowText();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getWrappedWidth()
+ */
+ public int getWrappedWidth()
+ {
+ return viewStyle.getWrappedWidth();
+ }
+
+ /**
+ * @param w
+ * @see jalview.api.ViewStyleI#setWrappedWidth(int)
+ */
+ public void setWrappedWidth(int w)
+ {
+ viewStyle.setWrappedWidth(w);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getCharHeight()
+ */
+ public int getCharHeight()
+ {
+ return viewStyle.getCharHeight();
+ }
+
+ /**
+ * @param h
+ * @see jalview.api.ViewStyleI#setCharHeight(int)
+ */
+ public void setCharHeight(int h)
+ {
+ viewStyle.setCharHeight(h);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getCharWidth()
+ */
+ public int getCharWidth()
+ {
+ return viewStyle.getCharWidth();
+ }
+
+ /**
+ * @param w
+ * @see jalview.api.ViewStyleI#setCharWidth(int)
+ */
+ public void setCharWidth(int w)
+ {
+ viewStyle.setCharWidth(w);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowBoxes()
+ */
+ public boolean getShowBoxes()
+ {
+ return viewStyle.getShowBoxes();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowUnconserved()
+ */
+ public boolean getShowUnconserved()
+ {
+ return viewStyle.getShowUnconserved();
+ }
+
+ /**
+ * @param showunconserved
+ * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
+ */
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ viewStyle.setShowUnconserved(showunconserved);
+ }
+
+ /**
+ * @param default1
+ * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
+ */
+ public void setSeqNameItalics(boolean default1)
+ {
+ viewStyle.setSeqNameItalics(default1);
+ }
+
+ /**
+ * @param selected
+ * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
+ */
+ public void setShowSeqFeaturesHeight(boolean selected)
+ {
+ viewStyle.setShowSeqFeaturesHeight(selected);
+ }
+
+ /**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ @Override
+ public char getGapCharacter()
+ {
+ return alignment.getGapCharacter();
+ }
+
+ protected String sequenceSetID;
+
+ /**
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+ protected ColumnSelection colSel = new ColumnSelection();
+
+ public boolean autoCalculateConsensus = true;
+
+ protected boolean autoCalculateStrucConsensus = true;
+
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected ColourSchemeI globalColourScheme = null;
+
+
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
|| cs instanceof Blosum62ColourScheme)
{
recalc = true;
- cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+ cs.setThreshold(viewStyle.getThreshold(),
+ ignoreGapsInConsensusCalculation);
}
else
{
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
+ sg.cs.setThreshold(viewStyle.getThreshold(),
+ getIgnoreGapsConsensus());
recalc = true;
}
else
}
/**
- * show non-conserved residues only
- */
- protected boolean showUnconserved = false;
-
- /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
*/
public boolean sortByTree = false;
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean showunconserved)
- {
- showUnconserved = showunconserved;
- }
-
- /**
- * @param showNonconserved
- * the showUnconserved to set
- */
- public void setShowunconserved(boolean displayNonconserved)
- {
- this.showUnconserved = displayNonconserved;
- }
/**
*
}
oldrfs.clear();
}
- /**
- * show the reference sequence in the alignment view
- */
- private boolean displayReferenceSeq=false;
- /**
- * colour according to the reference sequence defined on the alignment
- */
- private boolean colourByReferenceSeq=false;
-
@Override
public boolean isDisplayReferenceSeq()
{
- return alignment.hasSeqrep() && displayReferenceSeq;
+ return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
}
@Override
public void setDisplayReferenceSeq(boolean displayReferenceSeq)
{
- this.displayReferenceSeq = displayReferenceSeq;
+ viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
}
public boolean isColourByReferenceSeq()
{
- return alignment.hasSeqrep() && colourByReferenceSeq;
+ return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
}
- public void setColourByReferenceSeq(boolean colourByReferenceSeq)
- {
- this.colourByReferenceSeq = colourByReferenceSeq;
- }
@Override
public Color getSequenceColour(SequenceI seq)
}
/**
- * display setting for showing/hiding sequence features on alignment view
- */
- boolean showSequenceFeatures = false;
-
- /**
* set the flag
*
* @param b
@Override
public void setShowSequenceFeatures(boolean b)
{
- showSequenceFeatures = b;
+ viewStyle.setShowSequenceFeatures(b);
}
@Override
public boolean isShowSequenceFeatures()
{
- return showSequenceFeatures;
+ return viewStyle.isShowSequenceFeatures();
}
- boolean showSeqFeaturesHeight;
-
@Override
public void setShowSequenceFeaturesHeight(boolean selected)
{
- showSeqFeaturesHeight = selected;
+ viewStyle.setShowSeqFeaturesHeight(selected);
}
@Override
public boolean isShowSequenceFeaturesHeight()
{
- return showSeqFeaturesHeight;
+ return viewStyle.isShowSequenceFeaturesHeight();
}
- private boolean showAnnotation = true;
-
- private boolean rightAlignIds = false;
@Override
public void setShowAnnotation(boolean b)
{
- showAnnotation = b;
+ viewStyle.setShowAnnotation(b);
}
@Override
public boolean isShowAnnotation()
{
- return showAnnotation;
+ return viewStyle.isShowAnnotation();
}
@Override
public boolean isRightAlignIds()
{
- return rightAlignIds;
+ return viewStyle.isRightAlignIds();
}
@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);
}
}
--- /dev/null
+package jalview.viewmodel.styles;
+
+import jalview.api.ViewStyleI;
+
+import java.awt.Color;
+
+/**
+ * A container for holding alignment view properties. View properties are
+ * data-independent, which means they can be safely copied between views
+ * involving different alignment data without causing exceptions in the
+ * rendering system.
+ *
+ * @author jprocter
+ *
+ */
+public class ViewStyle implements ViewStyleI
+{
+
+ private boolean abovePIDThreshold = false;
+
+ int charHeight;
+
+ int charWidth;
+
+ /**
+ * gui state - changes to colour scheme propagated to all groups
+ */
+ private boolean colourAppliesToAllGroups;
+
+ /**
+ * colour according to the reference sequence defined on the alignment
+ */
+ private boolean colourByReferenceSeq = false;
+
+ boolean conservationColourSelected = false;
+
+ /**
+ * show the reference sequence in the alignment view
+ */
+ private boolean displayReferenceSeq = false;
+
+ private int increment;
+
+ /**
+ * display gap characters
+ */
+ boolean renderGaps = true;
+
+ private boolean rightAlignIds = false;
+
+ boolean scaleAboveWrapped = false;
+
+ boolean scaleLeftWrapped = true;
+
+ boolean scaleRightWrapped = true;
+
+ boolean seqNameItalics;
+
+ /**
+ * show annotation tracks on the alignment
+ */
+ private boolean showAnnotation = true;
+
+ /**
+ * render each residue in a coloured box
+ */
+ boolean showBoxes = true;
+
+ /**
+ * Colour sequence text
+ */
+ boolean showColourText = false;
+
+ /**
+ * show blue triangles
+ */
+ boolean showHiddenMarkers = true;
+
+ /**
+ * show /start-end in ID panel
+ */
+ boolean showJVSuffix = true;
+
+ /**
+ * scale features height according to score
+ */
+ boolean showSeqFeaturesHeight;
+
+ /**
+ * display setting for showing/hiding sequence features on alignment view
+ */
+ boolean showSequenceFeatures = false;
+
+ /**
+ * display sequence symbols
+ */
+ boolean showText = true;
+
+ /**
+ * show non-conserved residues only
+ */
+ protected boolean showUnconserved = false;
+
+ Color textColour = Color.black;
+
+ Color textColour2 = Color.white;
+
+ /**
+ * PID or consensus threshold
+ */
+ int threshold;
+
+ /**
+ * threshold for switching between textColour & textColour2
+ */
+ int thresholdTextColour = 0;
+
+ /**
+ * upper case characters in sequence are shown in bold
+ */
+ boolean upperCasebold = false;
+
+ /**
+ * @return the upperCasebold
+ */
+ @Override
+ public boolean isUpperCasebold()
+ {
+ return upperCasebold;
+ }
+
+ /**
+ * @param upperCasebold
+ * the upperCasebold to set
+ */
+ @Override
+ public void setUpperCasebold(boolean upperCasebold)
+ {
+ this.upperCasebold = upperCasebold;
+ }
+
+ /**
+ * flag for wrapping
+ */
+ boolean wrapAlignment = false;
+
+ /**
+ * number columns in wrapped alignment
+ */
+ int wrappedWidth;
+
+ /**
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
+ */
+ @Override
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ *
+ *
+ * @return flag indicating if colourchanges propagated to all groups
+ */
+ @Override
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
+ */
+ @Override
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * GUI State
+ *
+ * @return get scalar for bleaching colourschemes by conservation
+ */
+ @Override
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ @Override
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ @Override
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+
+ /**
+ * @return the textColour
+ */
+ @Override
+ public Color getTextColour()
+ {
+ return textColour;
+ }
+
+ /**
+ * @return the textColour2
+ */
+ @Override
+ public Color getTextColour2()
+ {
+ return textColour2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * @return the thresholdTextColour
+ */
+ @Override
+ public int getThresholdTextColour()
+ {
+ return thresholdTextColour;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ @Override
+ public boolean isColourByReferenceSeq()
+ {
+ return colourByReferenceSeq;
+ }
+
+ /**
+ * @return the conservationColourSelected
+ */
+ @Override
+ public boolean isConservationColourSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ @Override
+ public boolean isDisplayReferenceSeq()
+ {
+ return displayReferenceSeq;
+ }
+
+ /**
+ * @return the renderGaps
+ */
+ @Override
+ public boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
+
+ @Override
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ /**
+ * @return the seqNameItalics
+ */
+ @Override
+ public boolean isSeqNameItalics()
+ {
+ return seqNameItalics;
+ }
+
+ @Override
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * @return the showColourText
+ */
+ @Override
+ public boolean isShowColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * @return the showSeqFeaturesHeight
+ */
+ @Override
+ public boolean isShowSeqFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ @Override
+ public boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ @Override
+ public boolean isShowSequenceFeaturesHeight()
+ {
+
+ return showSeqFeaturesHeight;
+ }
+
+ /**
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
+ */
+ @Override
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+
+ /**
+ * @param value
+ * indicating if subsequent colourscheme changes will be propagated
+ * to all groups
+ */
+ @Override
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ @Override
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ this.colourByReferenceSeq = colourByReferenceSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * @param conservationColourSelected
+ * the conservationColourSelected to set
+ */
+ @Override
+ public void setConservationColourSelected(
+ boolean conservationColourSelected)
+ {
+ this.conservationColourSelected = conservationColourSelected;
+ }
+
+ /**
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
+ */
+ @Override
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ @Override
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ {
+ this.displayReferenceSeq = displayReferenceSeq;
+ }
+
+ /**
+ *
+ * @param inc
+ * set the scalar for bleaching colourschemes according to degree of
+ * conservation
+ */
+ @Override
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ @Override
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ *
+ *
+ * @param scaleRightWrapped
+ * - true or false
+ */
+
+ @Override
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ @Override
+ public void setSeqNameItalics(boolean italics)
+ {
+ seqNameItalics = italics;
+ }
+
+ @Override
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * @param showColourText
+ * the showColourText to set
+ */
+ @Override
+ public void setShowColourText(boolean showColourText)
+ {
+ this.showColourText = showColourText;
+ }
+
+ @Override
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ @Override
+ public void setShowSeqFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+
+ }
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ @Override
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ @Override
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved = showunconserved;
+ }
+
+ /**
+ * @param textColour
+ * the textColour to set
+ */
+ @Override
+ public void setTextColour(Color textColour)
+ {
+ this.textColour = textColour;
+ }
+
+ /**
+ * @param textColour2
+ * the textColour2 to set
+ */
+ @Override
+ public void setTextColour2(Color textColour2)
+ {
+ this.textColour2 = textColour2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * @param thresholdTextColour
+ * the thresholdTextColour to set
+ */
+ @Override
+ public void setThresholdTextColour(int thresholdTextColour)
+ {
+ this.thresholdTextColour = thresholdTextColour;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff