X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewJSApi.java;h=3f5dba06eb095b7f1115cac1dfb95230207a3c61;hb=2b4e37d6f7fda9d0437bee9ca67f4839dc9b9fa4;hp=7c9dee8ccaf1d08264fd999b0372df66576e6512;hpb=52af225db89e663347f69c9918501d5026488412;p=jalview.git
diff --git a/src/jalview/bin/JalviewJSApi.java b/src/jalview/bin/JalviewJSApi.java
index 7c9dee8..3f5dba0 100644
--- a/src/jalview/bin/JalviewJSApi.java
+++ b/src/jalview/bin/JalviewJSApi.java
@@ -12,7 +12,6 @@ import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
-import jalview.io.NewickFile;
import jalview.structure.SelectionSource;
import jalview.structure.VamsasSource;
@@ -44,8 +43,7 @@ public interface JalviewJSApi
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile);
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
public String arrayToSeparatorList(String[] array);
@@ -54,7 +52,7 @@ public interface JalviewJSApi
* an HTML page.
*
*
- * TODO: introduce abstract interface for
+ * TODO: introduce interface for
* jalview.appletgui.AlignFrame
*
* Most function arguments are strings, which contain serialised versions of
@@ -80,7 +78,7 @@ public interface JalviewJSApi
* @return
*/
- public abstract String getAlignment(String format);
+ public String getAlignment(String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
@@ -90,7 +88,7 @@ public interface JalviewJSApi
* @return
*/
- public abstract String getAlignment(String format, String suffix);
+ public String getAlignment(String format, String suffix);
/**
* get alignment displayed in alf as format
@@ -99,7 +97,7 @@ public interface JalviewJSApi
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
+ public String getAlignmentFrom(AlignFrame alf, String format);
/**
* get alignment displayed in alf as format with or without the jalview
@@ -110,8 +108,7 @@ public interface JalviewJSApi
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
- String suffix);
+ public String getAlignmentFrom(AlignFrame alf, String format, String suffix);
/**
* get a separator separated list of sequence IDs reflecting the order of the
@@ -120,7 +117,7 @@ public interface JalviewJSApi
* @return
*/
- public abstract String getAlignmentOrder();
+ public String getAlignmentOrder();
/**
* get a separator separated list of sequence IDs reflecting the order of the
@@ -129,7 +126,7 @@ public interface JalviewJSApi
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
+ public String getAlignmentOrderFrom(AlignFrame alf);
/**
* get a sep separated list of sequence IDs reflecting the order of the
@@ -140,7 +137,7 @@ public interface JalviewJSApi
* - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep);
/**
* get current alignment's annotation as an annotation file
@@ -148,7 +145,7 @@ public interface JalviewJSApi
* @return
*/
- public abstract String getAnnotation();
+ public String getAnnotation();
/**
* get alignment view alf's annotation as an annotation file
@@ -156,7 +153,7 @@ public interface JalviewJSApi
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrame alf);
+ public String getAnnotationFrom(AlignFrame alf);
public Object getAppletParameter(String name, boolean asString);
@@ -170,7 +167,7 @@ public interface JalviewJSApi
* @see jalview.appletgui.AlignFrame#getFeatureGroups();
*/
- public abstract String getFeatureGroups();
+ public String getFeatureGroups();
/**
* @param visible
@@ -178,7 +175,7 @@ public interface JalviewJSApi
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfState(boolean visible);
+ public String getFeatureGroupsOfState(boolean visible);
/**
* @param alf
@@ -187,8 +184,7 @@ public interface JalviewJSApi
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
- boolean visible);
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible);
/**
* @param alf
@@ -196,7 +192,7 @@ public interface JalviewJSApi
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups();
*/
- public abstract String getFeatureGroupsOn(AlignFrame alf);
+ public String getFeatureGroupsOn(AlignFrame alf);
/**
* get the sequence features in the given format (Jalview or GFF);
@@ -205,7 +201,7 @@ public interface JalviewJSApi
* @return
*/
- public abstract String getFeatures(String format);
+ public String getFeatures(String format);
/**
* get the sequence features in alf in the given format (Jalview or GFF);
@@ -214,28 +210,11 @@ public interface JalviewJSApi
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
+ public String getFeaturesFrom(AlignFrame alf, String format);
public Object getFrameForSource(VamsasSource source);
- public Hashtable getJSHashes();
-
- /**
- * Retrieve fragments of a large packet of data made available by JalviewLite.
- *
- * @param messageclass
- * @param viewId
- * @return next chunk of message
- */
-
- public abstract String getJsMessage(String messageclass, String viewId);
-
- Hashtable> getJSMessages();
-
- public Object getJSObject();
-
- public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
- AlignViewportI vp);
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
public String getParameter(String name);
@@ -244,7 +223,7 @@ public interface JalviewJSApi
* 'boolean not' character (""+0x00AC); or (¬);
*/
- public abstract String getSelectedSequences();
+ public SequenceI[] getSelectedSequences();
/**
* @param sep
@@ -253,7 +232,7 @@ public interface JalviewJSApi
* separator string
*/
- public abstract String getSelectedSequences(String sep);
+ public SequenceI[] getSelectedSequences(String sep);
/**
* get sequences selected in current AlignFrame and return their alignment in
@@ -269,8 +248,7 @@ public interface JalviewJSApi
* current selection
*/
- public abstract String getSelectedSequencesAsAlignment(String format,
- String suffix);
+ public String getSelectedSequencesAsAlignment(String format, String suffix);
/**
* get sequences selected in alf and return their alignment in format 'format'
@@ -285,8 +263,7 @@ public interface JalviewJSApi
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String suffix);
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
/**
* @param alf
@@ -295,7 +272,7 @@ public interface JalviewJSApi
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
+ public SequenceI[] getSelectedSequencesFrom(AlignFrame alf);
// BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
// creates an AlignmentPanel
@@ -305,7 +282,7 @@ public interface JalviewJSApi
// * @return
// */
//
- // public abstract AlignFrame newView();
+ // public AlignFrame newView();
//
// /**
// * create a new view named name and return the AlignFrame instance
@@ -314,7 +291,7 @@ public interface JalviewJSApi
// * @return
// */
//
- // public abstract AlignFrame newView(String name);
+ // public AlignFrame newView(String name);
//
// /**
// * create a new view on alf and return the AlignFrame instance
@@ -322,7 +299,7 @@ public interface JalviewJSApi
// * @param alf
// * @return
// */
- // public abstract AlignFrame newViewFrom(AlignFrame alf);
+ // public AlignFrame newViewFrom(AlignFrame alf);
//
// /**
// * create a new view named name on alf
@@ -331,7 +308,7 @@ public interface JalviewJSApi
// * @param name
// * @return
// */
- // public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
+ // public AlignFrame newViewFrom(AlignFrame alf, String name);
/**
* get list of selected sequence IDs separated by given separator
@@ -343,12 +320,9 @@ public interface JalviewJSApi
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf,
- String sep);
+ public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep);
- public Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame);
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
/**
* List separator string
@@ -356,7 +330,7 @@ public interface JalviewJSApi
* @return the separator
*/
- public abstract String getSeparator();
+ public String getSeparator();
public AlignViewportI getViewport();
@@ -371,8 +345,7 @@ public interface JalviewJSApi
* column or unaligned sequence position
*/
- public abstract void highlight(String sequenceId, String position,
- String alignedPosition);
+ public void highlight(String sequenceId, String position, String alignedPosition);
/**
*
@@ -384,8 +357,7 @@ public interface JalviewJSApi
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
- String position, String alignedPosition);
+ public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition);
/**
*
@@ -396,7 +368,7 @@ public interface JalviewJSApi
* @return null or new alignment frame
*/
- public abstract AlignFrame loadAlignment(String text, String title);
+ public AlignFrame loadAlignment(String text, String title);
/**
* add the given features or annotation to the current alignment
@@ -404,7 +376,7 @@ public interface JalviewJSApi
* @param annotation
*/
- public abstract void loadAnnotation(String annotation);
+ public void loadAnnotation(String annotation);
/**
* add the given features or annotation to the given alignment view
@@ -412,8 +384,7 @@ public interface JalviewJSApi
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrame alf,
- String annotation);
+ public void loadAnnotationFrom(AlignFrame alf, String annotation);
/**
* parse the given string as a jalview feature or GFF annotation file and
@@ -426,8 +397,7 @@ public interface JalviewJSApi
* be parsed from the string.
*/
- public abstract void loadFeatures(String features,
- boolean autoenabledisplay);
+ public void loadFeatures(String features, boolean autoenabledisplay);
/**
* parse the given string as a jalview feature or GFF annotation file and
@@ -441,15 +411,13 @@ public interface JalviewJSApi
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay);
+ public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay);
public boolean loadScoreFile(String sScoreFile) throws IOException;
public void newFeatureSettings();
- public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
- String[] chains, DataSourceType protocol);
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
/**
* public static method for JalviewJS API to open a PCAPanel without
@@ -474,8 +442,7 @@ public interface JalviewJSApi
* @return null, or the string "label.you_need_at_least_n_sequences" if number
* of sequences selected is inappropriate
*/
- public Object openTreePanel(AlignFrame af, String treeType,
- String modelName);
+ public Object openTreePanel(AlignFrame af, String treeType, String modelName);
/// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
@@ -495,8 +462,7 @@ public interface JalviewJSApi
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep);
+ public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep);
// get a string array from a list
@@ -511,7 +477,7 @@ public interface JalviewJSApi
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName);
+ public String orderBy(String order, String undoName);
/**
* re-order the current alignment using the given list of sequence IDs
@@ -526,7 +492,7 @@ public interface JalviewJSApi
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName, String sep);
+ public String orderBy(String order, String undoName, String sep);
/**
* process commandline arguments after the JavaScript application has started
@@ -534,7 +500,7 @@ public interface JalviewJSApi
* @param args
* @return
*/
- Object parseArguments(String[] args);
+ public Object parseArguments(String[] args);
// public boolean getDefaultParameter(String name, boolean def);
@@ -549,8 +515,7 @@ public interface JalviewJSApi
* @param listener
* (may be null);
*/
- public abstract void removeSelectionListener(AlignFrame af,
- String listener);
+ public void removeSelectionListener(AlignFrame af, String listener);
// public void setAlignPdbStructures(boolean defaultParameter);
@@ -561,8 +526,7 @@ public interface JalviewJSApi
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrame alf,
- String leftHandColumn);
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
/**
* adjust horizontal/vertical scroll to make the given location the top left
@@ -572,8 +536,7 @@ public interface JalviewJSApi
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrame alf, String topRow,
- String leftHandColumn);
+ public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn);
/**
* adjust vertical scroll to make the given row the top one for given view
@@ -581,7 +544,7 @@ public interface JalviewJSApi
* @param alf
* @param topRow
*/
- public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+ public void scrollViewToRowIn(AlignFrame alf, String topRow);
/**
* select regions of the currrent alignment frame
@@ -593,7 +556,7 @@ public interface JalviewJSApi
* string
*/
- public abstract void select(String sequenceIds, String columns);
+ public void select(String sequenceIds, String columns);
/**
* select regions of the currrent alignment frame
@@ -604,8 +567,7 @@ public interface JalviewJSApi
* separator between toselect fields
*/
- public abstract void select(String sequenceIds, String columns,
- String sep);
+ public void select(String sequenceIds, String columns, String sep);
/**
* select regions of the given alignment frame
@@ -616,8 +578,7 @@ public interface JalviewJSApi
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns);
/**
* select regions of the given alignment frame
@@ -628,12 +589,11 @@ public interface JalviewJSApi
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns, String sep);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep);
public String[] separatorListToArray(String list);
- public abstract void setFeatureGroupState(String groups, boolean state);
+ public void setFeatureGroupState(String groups, boolean state);
public void setFeatureGroupState(String[] groups, boolean state);
@@ -648,10 +608,9 @@ public interface JalviewJSApi
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean);
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state);
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state);
- public abstract void setSelectionListener(AlignFrame af, String listener);
+ public void setSelectionListener(AlignFrame af, String listener);
/**
* register a javascript function to handle any alignment selection events.
@@ -666,7 +625,7 @@ public interface JalviewJSApi
* single number or hyphenated range); that were selected);]
*/
- public abstract void setSelectionListener(String listener);
+ public void setSelectionListener(String listener);
/**
* List separator string
@@ -675,9 +634,9 @@ public interface JalviewJSApi
* the separator to set. empty string will reset separator to default
*/
- public abstract void setSeparator(String separator);
+ public void setSeparator(String separator);
- void showOverview();
+ public void showOverview();
public void updateForAnnotations();