*/
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
+
+ /**
+ * @return true if a reference sequence is set and should be displayed
+ */
+ public boolean isDisplayReferenceSeq();
+
+ /**
+ * @return set the flag for displaying reference sequences when they are
+ * available
+ */
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq);
+
+ /**
+ * @return true if colourschemes should render according to reference sequence
+ * rather than consensus if available
+ */
+ public boolean isColourByReferenceSeq();
+
+ /**
+ * @return true set flag for deciding if colourschemes should render according
+ * to reference sequence rather than consensus if available
+ */
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq);
void setSequenceColour(SequenceI seq, Color col);
SequenceGroup getSelectionGroup();
+ /**
+ * get the currently selected sequence objects or all the sequences in the
+ * alignment. TODO: change to List<>
+ *
+ * @return array of references to sequence objects
+ */
SequenceI[] getSequenceSelection();
void clearSequenceColours();
+ /**
+ * This method returns the visible alignment as text, as seen on the GUI, ie
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns.
+ *
+ * @return String[]
+ */
CigarArray getViewAsCigars(boolean selectedRegionOnly);
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @param selectedOnly
+ * boolean true to just return the selected view
+ * @return AlignmentView
+ */
AlignmentView getAlignmentView(boolean selectedOnly);
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @param selectedOnly
+ * boolean true to just return the selected view
+ * @param markGroups
+ * boolean true to annotate the alignment view with groups on the
+ * alignment (and intersecting with selected region if selectedOnly
+ * is true)
+ * @return AlignmentView
+ */
AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+ /**
+ * This method returns the visible alignment as text, as seen on the GUI, ie
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns.
+ *
+ * @return String[]
+ */
String[] getViewAsString(boolean selectedRegionOnly);
void setSelectionGroup(SequenceGroup sg);
List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly);
+ FeaturesDisplayedI getFeaturesDisplayed();
+
+ String getSequenceSetId();
+
+ boolean isShowSequenceFeatures();
+
+ void setShowSequenceFeatures(boolean b);
+
+ /**
+ *
+ * @param flag
+ * indicating if annotation panel shown below alignment
+ *
+ */
+ void setShowAnnotation(boolean b);
+
+ /**
+ * flag indicating if annotation panel shown below alignment
+ *
+ * @return
+ */
+ boolean isShowAnnotation();
+
+ boolean isRightAlignIds();
+
+ void setRightAlignIds(boolean rightAlignIds);
+
+ boolean areFeaturesDisplayed();
+
+ void setShowSequenceFeaturesHeight(boolean selected);
+
+ boolean isShowSequenceFeaturesHeight();
+
+ void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
+
+ void alignmentChanged(AlignmentViewPanel ap);
+
+ /**
+ * @return the padGaps
+ */
+ boolean isPadGaps();
+
+ /**
+ * @param padGaps
+ * the padGaps to set
+ */
+ void setPadGaps(boolean padGaps);
+
+ /**
+ * return visible region boundaries within given column range
+ *
+ * @param min
+ * first column (inclusive, from 0)
+ * @param max
+ * last column (exclusive)
+ * @return int[][] range of {start,end} visible positions TODO: change to list
+ * of int ranges
+ */
+ int[][] getVisibleRegionBoundaries(int min, int max);
+
+ /**
+ * This method returns an array of new SequenceI objects derived from the
+ * whole alignment or just the current selection with start and end points
+ * adjusted
+ *
+ * @note if you need references to the actual SequenceI objects in the
+ * alignment or currently selected then use getSequenceSelection()
+ * @return selection as new sequenceI objects
+ */
+ SequenceI[] getSelectionAsNewSequence();
+
+ void invertColumnSelection();
+
+ /**
+ * broadcast selection to any interested parties
+ */
+ void sendSelection();
+
+ /**
+ * calculate the row position for alignmentIndex if all hidden sequences were
+ * shown
+ *
+ * @param alignmentIndex
+ * @return adjusted row position
+ */
+ int adjustForHiddenSeqs(int alignmentIndex);
+
+ boolean hasHiddenRows();
+
/**
* Returns a viewport which holds the cDna for this (protein), or vice versa,
* or null if none is set.
*/
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/RAN, false if peptide.
+ * Answers true if viewport hosts DNA/RNA, else false.
*
* @return
*/
boolean isNucleotide();
+
}
git://source.jalview.org / jalview.git / blobdiff