1 ## public interface JalviewJSApi
3 # full list of available methods (from JalviewLiteJsApi):
5 public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
6 public String getAlignment(String format);
7 public String getAlignment(String format, String suffix);
8 public String getAlignmentFrom(AlignFrame alf, String format);
9 public String getAlignmentFrom(AlignFrame alf, String format, String suffix);
10 public String getAlignmentOrder();
11 public String getAlignmentOrderFrom(AlignFrame alf);
12 public String getAlignmentOrderFrom(AlignFrame alf, String sep);
13 public String getAnnotation();
14 public String getAnnotationFrom(AlignFrame alf);
15 public Object getAppletParameter(String name, boolean asString);
16 public URL getCodeBase();
17 public URL getDocumentBase();
18 public String getFeatureGroups();
19 public String getFeatureGroupsOfState(boolean visible);
20 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible);
21 public String getFeatureGroupsOn(AlignFrame alf);
22 public String getFeatures(String format);
23 public String getFeaturesFrom(AlignFrame alf, String format);
24 public Object getFrameForSource(VamsasSource source);
25 public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
26 public String getParameter(String name);
27 public String getSelectedSequences();
28 public String getSelectedSequences(String sep);
29 public String getSelectedSequencesAsAlignment(String format, String suffix);
30 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
31 public String getSelectedSequencesFrom(AlignFrame alf);
32 public String getSelectedSequencesFrom(AlignFrame alf, String sep);
33 public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
34 public String getSeparator();
35 public AlignViewportI getViewport();
36 public void highlight(String sequenceId, String position, String alignedPosition);
37 public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition);
38 public AlignFrame loadAlignment(String text, String title);
39 public void loadAnnotation(String annotation);
40 public void loadAnnotationFrom(AlignFrame alf, String annotation);
41 public void loadFeatures(String features, boolean autoenabledisplay);
42 public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay);
43 public boolean loadScoreFile(String sScoreFile) throws IOException;
44 public void newFeatureSettings();
45 public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
46 public Object openPcaPanel(AlignFrame af, String modelName);
47 public Object openTreePanel(AlignFrame af, String treeType, String modelName);
48 public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep);
49 public String orderBy(String order, String undoName);
50 public String orderBy(String order, String undoName, String sep);
51 public Object parseArguments(String[] args);
52 public boolean parseFeaturesFile(String param, DataSourceType protocol);
53 public void removeSelectionListener(AlignFrame af, String listener);
54 public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
55 public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn);
56 public void scrollViewToRowIn(AlignFrame alf, String topRow);
57 public void select(String sequenceIds, String columns);
58 public void select(String sequenceIds, String columns, String sep);
59 public void selectIn(AlignFrame alf, String sequenceIds, String columns);
60 public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep);
61 public void setFeatureGroupState(String groups, boolean state);
62 public void setFeatureGroupState(String[] groups, boolean state);
63 public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state);
64 public void setSelectionListener(AlignFrame af, String listener);
65 public void setSelectionListener(String listener);
66 public void setSeparator(String separator);
67 public void showOverview();
68 public void updateForAnnotations();
70 # addition available methods (from JalviewLite):
72 public static String getBuildDate()
73 public static String getInstallation()
74 public static String getVersion()
78 # proposed alias list:
80 - remove overloaded methods
81 - indicate null options
82 - use standard arrays; no need for special separators
83 - possibly return more actual objects, not just strings
85 public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
86 public String getAlignment(AlignFrame alf, String format, boolean includeStartEnd);
87 public String[] getAlignmentOrder(AlignFrame alf);
88 public String getAnnotation(AlignFrame alf);
89 public Object getAppletParameter(String name, boolean asString);
90 public URL getCodeBase();
91 public URL getDocumentBase();
92 public String[] getFeatureGroups();
93 public String[] getFeatureGroupsOfState(boolean visible);
94 public String getFeatures(AlignFrame alf, String format);
95 public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
96 public String getParameter(String name);
97 public String[] getSelectedSequences(AlignFrame alf);
98 public String[] getSelectedSequencesAsAlignment(AlignFrame alf, String format, boolean includeStartEnd);
99 public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
100 public AlignViewportI getViewport();
101 public void highlight(AlignFrame alf, String sequenceId, String position, String alignedPosition);
102 public AlignFrame loadAlignment(String text, String title);
103 public void loadAnnotation(AlignFrame alf, String annotation);
104 public boolean loadFeatures(AlignFrame alf, String features, boolean autoenabledisplay);
105 public boolean loadScoreFile(String sScoreFile) throws IOException;
106 public void newFeatureSettings();
107 public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
108 public Object openPcaPanel(AlignFrame af, String modelName);
109 public Object openTreePanel(AlignFrame af, String treeType, String modelName);
110 public String[] orderBy(AlignFrame alf, String order, String undoName);
111 public Object parseArguments(String[] args);
112 public boolean parseFeaturesFile(String param, DataSourceType protocol);
113 public void removeSelectionListener(AlignFrame af, String listener);
114 public void scrollViewTo(AlignFrame alf, String topRow, String leftHandColumn);
115 public void select(AlignFrame alf, String[] sequenceIds, String[] columns);
116 public void setFeatureGroupState(AlignFrame alf, String groups, boolean state);
117 public void setSelectionListener(AlignFrame af, String listener);
118 public void showOverview();
119 public void updateForAnnotations();
121 # unknown methods/shouldn't be in interface?
123 public Object getFrameForSource(VamsasSource source);
124 public void setSeparator(String separator);