X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FJalviewLiteJsApi.java;h=3ce2c9fad316e117272e72b18c26bd0b8cd115cc;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=44b1bc666854e68f7765b5e055e0748c47813a53;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git
diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 44b1bc6..3ce2c9f 100644
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -1,13 +1,13 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$);
+ * Copyright (C); $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
+ * of the License, or (at your option); any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
@@ -20,13 +20,13 @@
*/
package jalview.javascript;
-import jalview.appletgui.AlignFrame;
+import jalview.api.AlignFrameI;
/**
* The following public methods may be called
* externally, eg via javascript in an HTML page.
*
- *
TODO: introduce abstract interface for jalview.appletgui.AlignFrame
+ *
TODO: introduce abstract interface for jalview.appletgui.AlignFrameI
*
* Most function arguments are strings, which contain serialised versions of lists.
* Lists of things are separated by a separator character - either the default or a user supplied one.
@@ -42,7 +42,7 @@ public interface JalviewLiteJsApi
/**
* @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC) or (¬)
+ * 'boolean not' character (""+0x00AC); or (¬);
*/
public abstract String getSelectedSequences();
@@ -56,12 +56,12 @@ public interface JalviewLiteJsApi
/**
* @param alf
- * alignframe containing selection
+ * AlignFrameI containing selection
* @return String list of selected sequence IDs, each terminated by current
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf);
/**
* get list of selected sequence IDs separated by given separator
@@ -73,7 +73,8 @@ public interface JalviewLiteJsApi
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf, String sep);
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf,
+ String sep);
/**
*
@@ -98,7 +99,7 @@ public interface JalviewLiteJsApi
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
+ public abstract void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition);
/**
@@ -120,7 +121,8 @@ public interface JalviewLiteJsApi
* @param sep
* separator between toselect fields
*/
- public abstract void select(String sequenceIds, String columns, String sep);
+ public abstract void select(String sequenceIds, String columns,
+ String sep);
/**
* select regions of the given alignment frame
@@ -131,7 +133,7 @@ public interface JalviewLiteJsApi
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns);
/**
@@ -143,11 +145,11 @@ public interface JalviewLiteJsApi
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns, String sep);
/**
- * get sequences selected in current alignFrame and return their alignment in
+ * get sequences selected in current AlignFrameI and return their alignment in
* format 'format' either with or without suffix
*
* @param alf
@@ -176,7 +178,8 @@ public interface JalviewLiteJsApi
* current selection
*/
public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrame alf, String format, String suffix);
+ AlignFrameI alf,
+ String format, String suffix);
/**
* get a separator separated list of sequence IDs reflecting the order of the
@@ -193,7 +196,7 @@ public interface JalviewLiteJsApi
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
+ public abstract String getAlignmentOrderFrom(AlignFrameI alf);
/**
* get a sep separated list of sequence IDs reflecting the order of the
@@ -204,7 +207,8 @@ public interface JalviewLiteJsApi
* - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
+ public abstract String getAlignmentOrderFrom(AlignFrameI alf,
+ String sep);
/**
* re-order the current alignment using the given list of sequence IDs
@@ -230,7 +234,8 @@ public interface JalviewLiteJsApi
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName, String sep);
+ public abstract String orderBy(String order, String undoName,
+ String sep);
/**
* re-order the given alignment using the given list of sequence IDs separated
@@ -245,12 +250,12 @@ public interface JalviewLiteJsApi
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
+ public abstract String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep);
/**
* get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
- * PFAM - see jalview.io.AppletFormatAdapter for full list)
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
*
* @param format
* @return
@@ -264,7 +269,7 @@ public interface JalviewLiteJsApi
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
+ public abstract String getAlignmentFrom(AlignFrameI alf, String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
@@ -284,7 +289,7 @@ public interface JalviewLiteJsApi
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
+ public abstract String getAlignmentFrom(AlignFrameI alf, String format,
String suffix);
/**
@@ -300,11 +305,12 @@ public interface JalviewLiteJsApi
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrame alf, String annotation);
+ public abstract void loadAnnotationFrom(AlignFrameI alf,
+ String annotation);
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the current alignFrame
+ * optionally enable feature display on the current AlignFrameI
*
* @param features
* - gff or features file
@@ -317,7 +323,7 @@ public interface JalviewLiteJsApi
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given alignFrame.
+ * optionally enable feature display on the given AlignFrameI.
*
* @param alf
* @param features
@@ -327,11 +333,11 @@ public interface JalviewLiteJsApi
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
+ public abstract boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay);
/**
- * get the sequence features in the given format (Jalview or GFF)
+ * get the sequence features in the given format (Jalview or GFF);
*
* @param format
* @return
@@ -339,13 +345,13 @@ public interface JalviewLiteJsApi
public abstract String getFeatures(String format);
/**
- * get the sequence features in alf in the given format (Jalview or GFF)
+ * get the sequence features in alf in the given format (Jalview or GFF);
*
* @param alf
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
+ public abstract String getFeaturesFrom(AlignFrameI alf, String format);
/**
* get current alignment's annotation as an annotation file
@@ -360,30 +366,30 @@ public interface JalviewLiteJsApi
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrame alf);
+ public abstract String getAnnotationFrom(AlignFrameI alf);
/**
- * create a new view and return the alignFrame instance
+ * create a new view and return the AlignFrameI instance
*
* @return
*/
- public abstract AlignFrame newView();
+ public abstract AlignFrameI newView();
/**
- * create a new view named name and return the alignFrame instance
+ * create a new view named name and return the AlignFrameI instance
*
* @param name
* @return
*/
- public abstract AlignFrame newView(String name);
+ public abstract AlignFrameI newView(String name);
/**
- * create a new view on alf and return the alignFrame instance
+ * create a new view on alf and return the AlignFrameI instance
*
* @param alf
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf);
/**
* create a new view named name on alf
@@ -392,7 +398,7 @@ public interface JalviewLiteJsApi
* @param name
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf, String name);
/**
*
@@ -402,15 +408,15 @@ public interface JalviewLiteJsApi
* window title
* @return null or new alignment frame
*/
- public abstract AlignFrame loadAlignment(String text, String title);
+ public abstract AlignFrameI loadAlignment(String text, String title);
/**
* register a javascript function to handle any alignment mouseover events
*
* @param listener
* name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame,String(sequence id),String(column in
- * alignment), String(position in sequence)]
+ * [jalview.appletgui.AlignFrameI,String(sequence id);,String(column
+ * in alignment);, String(position in sequence);]
*/
public abstract void setMouseoverListener(String listener);
@@ -418,12 +424,13 @@ public interface JalviewLiteJsApi
* register a javascript function to handle mouseover events
*
* @param af
- * (null or specific alignframe for which events are to be listened
- * for)
+ * (null or specific AlignFrameI for which events are to be listened
+ * for);
* @param listener
* name of javascript function
*/
- public abstract void setMouseoverListener(AlignFrame af, String listener);
+ public abstract void setMouseoverListener(AlignFrameI af,
+ String listener);
/**
* register a javascript function to handle any alignment selection events.
@@ -432,14 +439,15 @@ public interface JalviewLiteJsApi
*
* @param listener
* name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame, String(sequence set id),
- * String(separator separated list of sequences which were selected),
- * String(separator separated list of column ranges (i.e. single
- * number or hyphenated range) that were selected)]
+ * [jalview.appletgui.AlignFrameI, String(sequence set id);,
+ * String(separator separated list of sequences which were
+ * selected);, String(separator separated list of column ranges (i.e.
+ * single number or hyphenated range); that were selected);]
*/
public abstract void setSelectionListener(String listener);
- public abstract void setSelectionListener(AlignFrame af, String listener);
+ public abstract void setSelectionListener(AlignFrameI af,
+ String listener);
/**
* register a javascript function to handle events normally routed to a Jmol
@@ -447,25 +455,26 @@ public interface JalviewLiteJsApi
*
* @param listener
* - javascript function (arguments are variable, see
- * jalview.javascript.MouseOverStructureListener for full details)
+ * jalview.javascript.MouseOverStructureListener for full details);
* @param modelSet
* - separator separated list of PDB file URIs that this viewer is
* handling. These files must be in the same order they appear in
- * Jmol (e.g. first one is frame 1, second is frame 2, etc).
+ * Jmol (e.g. first one is frame 1, second is frame 2, etc);.
* @see jalview.javascript.MouseOverStructureListener
*/
- public abstract void setStructureListener(String listener, String modelSet);
+ public abstract void setStructureListener(String listener,
+ String modelSet);
/**
* remove any callback using the given listener function and associated with
- * the given alignFrame (or null for all callbacks)
+ * the given AlignFrameI (or null for all callbacks);
*
* @param af
- * (may be null)
+ * (may be null);
* @param listener
- * (may be null)
+ * (may be null);
*/
- public abstract void removeJavascriptListener(AlignFrame af,
+ public abstract void removeJavascriptListener(AlignFrameI af,
String listener);
/**
@@ -480,10 +489,10 @@ public interface JalviewLiteJsApi
String pdbfile);
/**
- * bind a pdb file to a sequence in the given alignFrame.
+ * bind a pdb file to a sequence in the given AlignFrameI.
*
* @param alFrame
- * - null or specific alignFrame. This specifies the dataset that
+ * - null or specific AlignFrameI. This specifies the dataset that
* will be searched for a seuqence called sequenceId
* @param sequenceId
* - sequenceId within the dataset.
@@ -495,7 +504,7 @@ public interface JalviewLiteJsApi
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ public abstract boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile);
/**
@@ -506,7 +515,7 @@ public interface JalviewLiteJsApi
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrame alf, String topRow,
+ public abstract void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn);
/**
@@ -515,7 +524,7 @@ public interface JalviewLiteJsApi
* @param alf
* @param topRow
*/
- public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+ public abstract void scrollViewToRowIn(AlignFrameI alf, String topRow);
/**
* adjust horizontal scroll to make the given column the left one in the given
@@ -524,28 +533,28 @@ public interface JalviewLiteJsApi
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrame alf,
+ public abstract void scrollViewToColumnIn(AlignFrameI alf,
String leftHandColumn);
/**
*
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
public abstract String getFeatureGroups();
/**
* @param alf
- * alignframe to get feature groups on
+ * AlignFrameI to get feature groups on
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
- public abstract String getFeatureGroupsOn(AlignFrame alf);
+ public abstract String getFeatureGroupsOn(AlignFrameI alf);
/**
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
public abstract String getFeatureGroupsOfState(boolean visible);
@@ -554,9 +563,9 @@ public interface JalviewLiteJsApi
* align frame to get groups of state visible
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
+ public abstract String getFeatureGroupsOfStateOn(AlignFrameI alf,
boolean visible);
/**
@@ -564,11 +573,12 @@ public interface JalviewLiteJsApi
* tab separated list of group names
* @param state
* true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
+ * @see jalview.appletgui.AlignFrameI#setFeatureGroupState(java.lang.String[],
+ * boolean);
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf,
- String groups, boolean state);
+ public abstract void setFeatureGroupStateOn(AlignFrameI alf,
+ String groups,
+ boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);
@@ -596,4 +606,24 @@ public interface JalviewLiteJsApi
*/
public abstract String getJsMessage(String messageclass, String viewId);
+ /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
+
+ // get selected sequences as alignment as format with or without start-end
+ // suffix
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix);
+
+ // get selected sequences as alignment from given view as format with or
+ // without start-end suffix
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix);
+
+ public String arrayToSeparatorList(String[] array);
+
+ // get a string array from a list
+ public String[] separatorListToArray(String list);
+
+ // debug flag - controls output to standard out
+ public static boolean debug = false;
+
}