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 String getParameter(String name);
26 public String getSelectedSequences();
27 public String getSelectedSequences(String sep);
28 public String getSelectedSequencesAsAlignment(String format, String suffix);
29 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
30 public String getSelectedSequencesFrom(AlignFrame alf);
31 public String getSelectedSequencesFrom(AlignFrame alf, String sep);
32 public String getSeparator();
33 public AlignViewportI getViewport();
34 public void highlight(String sequenceId, String position, String alignedPosition);
35 public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition);
36 public AlignFrame loadAlignment(String text, String title);
37 public void loadAnnotation(String annotation);
38 public void loadAnnotationFrom(AlignFrame alf, String annotation);
39 public void loadFeatures(String features, boolean autoenabledisplay);
40 public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay);
41 public boolean loadScoreFile(String sScoreFile) throws IOException;
42 public void newFeatureSettings();
43 public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
44 public Object openPcaPanel(AlignFrame af, String modelName);
45 public Object openTreePanel(AlignFrame af, String treeType, String modelName);
46 public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep);
47 public String orderBy(String order, String undoName);
48 public String orderBy(String order, String undoName, String sep);
49 public Object parseArguments(String[] args);
50 public boolean parseFeaturesFile(String param, DataSourceType protocol);
51 public void removeSelectionListener(AlignFrame af, String listener);
52 public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
53 public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn);
54 public void scrollViewToRowIn(AlignFrame alf, String topRow);
55 public void select(String sequenceIds, String columns);
56 public void select(String sequenceIds, String columns, String sep);
57 public void selectIn(AlignFrame alf, String sequenceIds, String columns);
58 public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep);
59 public void setFeatureGroupState(String groups, boolean state);
60 public void setFeatureGroupState(String[] groups, boolean state);
61 public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state);
62 public void setSelectionListener(AlignFrame af, String listener);
63 public void setSelectionListener(String listener);
64 public void setSeparator(String separator);
65 public void showOverview();
66 public void updateForAnnotations();
68 ## addition available methods (from JalviewLite):
70 public static String getBuildDate()
71 public static String getInstallation()
72 public static String getVersion()
76 ## proposed alias list:
78 - remove overloaded methods
79 - indicate null options
80 - use standard arrays; no need for special separators
81 - possibly return more actual objects, not just strings
82 - moves AlignFrame to last parameter, as it is likely to be unnecessary
84 public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile, AlignFrame alFrame);
85 public String getAlignment(String format, boolean addSuffix, AlignFrame alf);
86 public String[] getAlignmentOrder(AlignFrame alf);
87 public String getAnnotation(AlignFrame alf);
88 public URL getCodeBase();
89 public URL getDocumentBase();
90 public String[] getFeatureGroups(AlignFrame alf);
91 public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf);
92 public String getFeatures(String format, AlignFrame alf);
93 public String getParameter(String name);
94 public Object getParameterAsObject(String name);
95 public SequenceI[] getSelectedSequences(AlignFrame alf);
96 public AlignFrame newView();
97 public AlignFrame newView(String name);
98 public AlignFrame newViewFrom(AlignFrame alf);
99 public AlignFrame newViewFrom(AlignFrame alf, String name);
100 public String getSelectedSequencesAsAlignment(String format, boolean addSuffix, AlignFrame alf);
101 public void highlight(String sequenceId, String position, String alignedPosition, AlignFrame alf);
102 public AlignFrame loadAlignment(String data, String title, int width, int height);
103 public void loadAnnotation(String annotation, AlignFrame alf);
104 public boolean loadFeatures(String features, boolean autoenabledisplay, AlignFrame alf);
105 public boolean loadScoreFile(String sScoreFile, AlignFrame alf);
106 public Object openPcaPanel(String modelName, AlignFrame alf);
107 public Object openTreePanel(String treeType, String modelName, AlignFrame alf);
108 public boolean orderAlignment(String[] ids, String undoName, AlignFrame alf);
109 public Object parseArguments(String[] args);
110 public void removeSelectionListener(String listener, AlignFrame af);
111 public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf);
112 public void select(String[] sequenceIds, String[] columns, AlignFrame alf);
113 public void setFeatureGroupState(String[] groups, boolean state, AlignFrame alf);
114 public void setSelectionListener(String listener, AlignFrame alf);
115 public void showOverview();
116 public void showStructure(String pdbID, String fileType, AlignFrame alf);
119 # unknown methods/shouldn't be in interface?
121 public Object getFrameForSource(VamsasSource source);
122 public void setSeparator(String separator);