action.remove = Remove
action.remove_redundancy = Remove Redundancy...
action.pairwise_alignment = Pairwise Alignment
- action.by_rna_helixes = By RNA Helices
action.user_defined = User Defined...
action.by_conservation = By Conservation
action.wrap = Wrap
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
label.structures_manager = Structures Manager
label.nickname = Nickname:
- label.url = URL:
+ label.url = URL
+ label.url\: = URL:
label.input_file_url = Enter URL or Input File
label.select_feature = Select feature
label.name = Name
label.score_model_enhconservation = Physicochemical property conservation
label.status_bar = Status bar
label.out_to_textbox = Output to Textbox
- label.clustalx = Clustalx
+ # delete Clustal - use FileFormat name instead
label.clustal = Clustal
- label.zappo = Zappo
- label.taylor = Taylor
+ # label.colourScheme_<schemeName> as in JalviewColourScheme
+ label.colourScheme_clustal = Clustalx
+ label.colourScheme_blosum62 = BLOSUM62 Score
+ label.colourScheme_%_identity = Percentage Identity
+ label.colourScheme_zappo = Zappo
+ label.colourScheme_taylor = Taylor
+ label.colourScheme_hydrophobic = Hydrophobicity
+ label.colourScheme_helix_propensity = Helix Propensity
+ label.colourScheme_strand_propensity = Strand Propensity
+ label.colourScheme_turn_propensity = Turn Propensity
+ label.colourScheme_buried_index = Buried Index
+ label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
+ label.colourScheme_nucleotide = Nucleotide
+ label.colourScheme_t-coffee_scores = T-Coffee Scores
+ label.colourScheme_rna_helices = By RNA Helices
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.pfam = PFAM
label.pileup = Pileup
label.pir = PIR
- label.hydrophobicity = Hydrophobicity
- label.helix_propensity = Helix Propensity
- label.strand_propensity = Strand Propensity
- label.turn_propensity = Turn Propensity
- label.buried_index = Buried Index
- label.purine_pyrimidine = Purine/Pyrimidine
- label.percentage_identity = Percentage Identity
- label.blosum62 = BLOSUM62
- label.blosum62_score = BLOSUM62 Score
- label.tcoffee_scores = T-Coffee Scores
- label.average_distance_bloslum62 = Average Distance Using BLOSUM62
+ label.average_distance_blosum62 = Average Distance Using BLOSUM62
label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
label.show_annotations = Show annotations
label.hide_annotations = Hide annotations
label.add_reference_annotations = Add reference annotations
label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).<br>Accepts regular expressions - search Help for 'regex' for details.
label.colour_text = Colour Text
- label.show_non_conversed = Show nonconserved
+ label.show_non_conserved = Show nonconserved
label.overview_window = Overview Window
label.none = None
label.above_identity_threshold = Above Identity Threshold
label.style = Style:
label.calculating = Calculating....
label.modify_conservation_visibility = Modify conservation visibility
- label.colour_residues_above_occurence = Colour residues above % occurence
+ label.colour_residues_above_occurrence = Colour residues above % occurrence
label.set_this_label_text = set this label text
label.sequences_from = Sequences from {0}
label.successfully_loaded_file = Successfully loaded file {0}
label.vamsas_document_import_failed = Vamsas Document Import Failed
label.couldnt_locate = Couldn't locate {0}
label.url_not_found = URL not found
- label.no_link_selected = No link selected
label.new_sequence_url_link = New sequence URL link
label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
label.wrapped_view_no_edit = Wrapped view - no edit
label.standard_databases = Standard Databases
label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
- label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
+ label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
label.connect_to_session = Connect to session {0}
label.threshold_feature_display_by_score = Threshold the feature display by score.
label.threshold_feature_no_threshold = No Threshold
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
label.let_chimera_manage_structure_colours = Let Chimera manage structure colours
+ label.fetch_chimera_attributes = Fetch Chimera attributes
+ label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
label.index_web_services_menu_by_host_site = Index web services in menu by the host site
label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
label.structure = Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.view_rna_structure = VARNA 2D Structure
- label.clustalx_colours = Clustalx colours
- label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.pdb_file = PDB file
label.colour_with_jmol = Colour with Jmol
label.colour_with_chimera = Colour with Chimera
- label.align_structures = Align Structures
+ label.superpose_structures = Superpose Structures
+ error.superposition_failed = Superposition failed: {0}
+ label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
label.jmol = Jmol
label.chimera = Chimera
+ label.create_chimera_attributes = Write Jalview features
+ label.create_chimera_attributes_tip = Set Chimera residue attributes for visible features
+ label.attributes_set = {0} attribute values set on Chimera
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu
label.case_sensitive = Case Sensitive
- label.lower_case_colour = Lower Case Colour
+ label.lower_case_colour = Colour All Lower Case
+ label.lower_case_tip = Chosen colour applies to all lower case symbols
label.index_by_host = Index by Host
label.index_by_type = Index by Type
label.enable_jabaws_services = Enable JABAWS Services
label.points_for_params = Points for {0}
label.transformed_points_for_params = Transformed points for {0}
label.graduated_color_for_params = Graduated Feature Colour for {0}
- label.select_backgroud_colour = Select Background Colour
+ label.select_background_colour = Select Background Colour
label.invalid_font = Invalid Font
label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.
- error.implementation_error_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0}
error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
exception.ssm_context_is_null = SSM context is null
error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence
exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0}
exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0}
exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0}
- exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0}
exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0}
exception.mismatched_closing_char = Mismatched closing character {0}
exception.mismatched_opening_char = Mismatched opening character {0} at {1}
exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console
exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding
exception.overwriting_jalview_id_binding = Overwriting jalview id binding
- error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string
exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream
exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2}
exception.problem_opening_file = Problem opening {0} : {1}
action.export_hidden_sequences = Export Hidden Sequences
action.export_features = Export Features
label.export_settings = Export Settings
- label.save_as_biojs_html = Save as BioJs HTML
label.pdb_web-service_error = PDB Web-service Error
label.structure_chooser_manual_association = Structure Chooser - Manual association
label.structure_chooser_filter_time = Structure Chooser - Filter time ({0})
label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
label.do_not_display_again = Do not display this message again
+ exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+ exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+ label.filter = Filter text:
+ action.customfilter = Custom only
+ action.showall = Show All
+ label.insert = Insert:
+ action.seq_id = $SEQUENCE_ID$
+ action.db_acc = $DB_ACCESSION$
+ label.primary = Double Click
+ label.inmenu = In Menu
+ label.id = ID
+ label.database = Database
+ label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
+ label.edit_sequence_url_link = Edit sequence URL link
+ warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
+ label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
++<<<<<<< HEAD
+label.phyre2_model_prediction = 3D Protein Model prediction with Phyre2
+label.run_phyre2_prediction = Run Phyre2 Prediction
- status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
++status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
++=======
+ label.urllinks = Links
++>>>>>>> develop
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
+ import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
- import jalview.schemes.RNAHelicesColourChooser;
+ import jalview.schemes.RNAHelicesColour;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
}
if (viewport.getAlignment().isNucleotide())
{
+ conservationMenuItem.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
viewport.updateStrucConsensus(alignPanel);
if (viewport.getAlignment().hasRNAStructure())
{
{
RNAHelixColour.setEnabled(false);
purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
}
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
// }
else if (source == RNAHelixColour)
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ changeColour(new RNAHelicesColour(viewport.getAlignment()));
+ // new RNAHelicesColourChooser(viewport, alignPanel);
}
else if (source == modifyPID)
{
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
- FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
fileFormat, viewport.getAlignment(),
viewport.getShowJVSuffix()));
@Override
public void changeColour(ColourSchemeI cs)
{
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
- cs, "Background"));
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationApplied(true);
- viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- else
- {
- cs.setConservationApplied(false);
- }
- }
viewport.setGlobalColourScheme(cs);
alignPanel.paintAlignment(true);
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
}
protected void conservationMenuItem_actionPerformed()
{
- viewport.setConservationSelected(conservationMenuItem.getState());
+ boolean selected = conservationMenuItem.getState();
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setState(false);
+ // viewport.setAbovePIDThreshold(false);
+ // abovePIDThreshold.setState(false);
changeColour(viewport.getGlobalColourScheme());
- modifyConservation_actionPerformed();
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
public void abovePIDThreshold_actionPerformed()
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
- conservationMenuItem.setState(false);
- viewport.setConservationSelected(false);
+ boolean selected = abovePIDThreshold.getState();
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ // conservationMenuItem.setState(false);
+ // viewport.setConservationSelected(false);
changeColour(viewport.getGlobalColourScheme());
- modifyPID_actionPerformed();
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
public void sortPairwiseMenuItem_actionPerformed()
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
MenuItem item = new MenuItem(ff);
.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconservedMenuItem.addItemListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+ clustalColour.setLabel(MessageManager
+ .getString("label.colourScheme_clustal"));
clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.setLabel(MessageManager
+ .getString("label.colourScheme_zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
taylorColour.addActionListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
+ .getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
+ .getString("label.colourScheme_strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
- .getString("label.purine_pyrimidine"));
+ .getString("label.colourScheme_purine/pyrimidine"));
purinePyrimidineColour.addActionListener(this);
// RNAInteractionColour.setLabel(MessageManager
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(MessageManager
- .getString("action.by_rna_helixes"));
+ .getString("label.colourScheme_rna_helices"));
RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(MessageManager
- .getString("label.percentage_identity"));
+ .getString("label.colourScheme_%_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(MessageManager
- .getString("label.blosum62_score"));
+ .getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour
- .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setLabel(MessageManager
+ .getString("label.colourScheme_t-coffee_scores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
abovePIDThreshold.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.setLabel(MessageManager
+ .getString("label.colourScheme_nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
.getString("label.modify_identity_threshold"));
+ modifyPID.setEnabled(abovePIDThreshold.getState());
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_threshold"));
+ modifyConservation.setEnabled(conservationMenuItem.getState());
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_bloslum62"));
+ .getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem.setLabel(MessageManager
.getString("label.neighbour_blosum62"));
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
- import jalview.io.FileParse;
import jalview.io.DataSourceType;
+ import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
+ MenuItem zappo = new MenuItem(
+ MessageManager.getString("label.colourScheme_zappo"));
- MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
+ MenuItem taylor = new MenuItem(
+ MessageManager.getString("label.colourScheme_taylor"));
MenuItem hydro = new MenuItem(
- MessageManager.getString("label.hydrophobicity"));
+ MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.helix_propensity"));
+ MessageManager.getString("label.colourScheme_helix_propensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.strand_propensity"));
+ MessageManager.getString("label.colourScheme_strand_propensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.turn_propensity"));
+ MessageManager.getString("label.colourScheme_turn_propensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.buried_index"));
+ MessageManager.getString("label.colourScheme_buried_index"));
MenuItem purinepyrimidine = new MenuItem(
- MessageManager.getString("label.purine_pyrimidine"));
+ MessageManager.getString("label.colourScheme_purine/pyrimidine"));
MenuItem user = new MenuItem(
MessageManager.getString("label.user_defined_colours"));
{
reader = StructureSelectionManager.getStructureSelectionManager(
ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
- protocol);
+ protocol, null);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
public void updateTitleAndMenus()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ if (jmb.hasFileLoadingError())
{
repaint();
return;
*/
package jalview.ext.jmol;
- import jalview.api.AlignmentViewPanel;
+ import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+ import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Container;
import java.net.URL;
import java.security.AccessControlException;
import java.util.ArrayList;
+ import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
Hashtable<String, String> chainFile;
- public String fileLoadingError;
-
/*
* the default or current model displayed if the model cannot be identified
* from the selection message
releaseUIResources();
}
+ @Override
public void colourByChain()
{
colourBySequence = false;
evalStateCommand("select *;color chain");
}
+ @Override
public void colourByCharge()
{
colourBySequence = false;
}
/**
- * Construct and send a command to align structures against a reference
- * structure, based on one or more sequence alignments
- *
- * @param _alignment
- * an array of alignments to process
- * @param _refStructure
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param _hiddenCols
- * an array of corresponding hidden columns for each alignment
+ * {@inheritDoc}
*/
- public void superposeStructures(AlignmentI[] _alignment,
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
while (viewer.isScriptExecuting())
String[] files = getPdbFile();
if (!waitForFileLoad(files))
{
- return;
+ return null;
}
StringBuilder selectioncom = new StringBuilder(256);
nSeconds = " " + (2.0 / files.length) + " ";
// if (nSeconds).substring(0,5)+" ";
}
+
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
// nSeconds = " ";
}
/*
- * 'matched' array will hold 'true' for visible alignment columns where
+ * 'matched' bit j will be set for visible alignment columns j where
* all sequences have a residue with a mapping to the PDB structure
*/
- // TODO could use a BitSet for matched
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
SuperposeData[] structures = new SuperposeData[files.length];
}
String[] selcom = new String[files.length];
- int nmatched = 0;
- for (boolean b : matched)
- {
- if (b)
- {
- nmatched++;
- }
- }
+ int nmatched = matched.cardinality();
if (nmatched < 4)
{
- // TODO: bail out here because superposition illdefined?
+ return (MessageManager.formatMessage(
+ "label.insufficient_residues",
+ nmatched));
}
/*
boolean run = false;
StringBuilder molsel = new StringBuilder();
molsel.append("{");
- for (int r = 0; r < matched.length; r++)
+
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
{
- if (matched[r])
+ int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
+ if (lpos != pdbResNo - 1)
{
- int pdbResNo = structures[pdbfnum].pdbResNo[r];
- if (lpos != pdbResNo - 1)
+ // discontinuity
+ if (lpos != -1)
{
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- molsel.append("|");
- }
- run = false;
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("|");
}
- else
+ run = false;
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
{
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
- }
- run = true;
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
}
- lpos = pdbResNo;
+ run = true;
}
+ lpos = pdbResNo;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
/*
* add final selection phrase
+ selectioncom.toString() + "); cartoons; ");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
+
+ return null;
}
public void evalStateCommand(String command)
}
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
{
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (!colourBySequence || !isLoadingFinished())
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
{
for (String cbyseq : cpdbbyseq.commands)
{
* @param files
* @param sr
* @param fr
- * @param alignment
+ * @param viewport
* @return
*/
+ @Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ AlignViewportI viewport)
{
return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, alignment);
+ getSequence(), sr, fr, viewport);
}
/**
}
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
* instruct the Jalview binding to update the pdbentries vector if necessary
* prior to matching the jmol view's contents to the list of structure files
* Jalview knows about.
return null;
}
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
+
// ///////////////////////////////
// JmolStatusListener
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE);
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
return chainNames;
}
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
command.append("select *;color white;");
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
- for (String res : residueSet)
+ for (String resName : residueSet)
{
- Color col = cs.findColour(res.charAt(0));
- command.append("select " + res + ";color[" + col.getRed() + ","
+ char res = resName.length() == 3 ? ResidueProperties
+ .getSingleCharacterCode(resName) : resName.charAt(0);
+ Color col = cs.findColour(res, 0, null, null, 0f);
+ command.append("select " + resName + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
protected org.jmol.api.JmolAppConsoleInterface console = null;
+ @Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
--- /dev/null
+ package jalview.ext.rbvi.chimera;
+
+ import jalview.util.RangeComparator;
+
+ import java.util.ArrayList;
+ import java.util.Collections;
+ import java.util.Iterator;
+ import java.util.List;
+ import java.util.Map;
+ import java.util.TreeMap;
+
+ /**
+ * A class to model a Chimera atomspec pattern, for example
+ *
+ * <pre>
+ * #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
+ * </pre>
+ *
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ *
+ * <pre>
+ * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * </pre>
+ */
+ public class AtomSpecModel
+ {
+ private Map<Integer, Map<String, List<int[]>>> atomSpec;
+
+ /**
+ * Constructor
+ */
+ public AtomSpecModel()
+ {
+ atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
+ }
+
+ /**
+ * Adds one contiguous range to this atom spec
+ *
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public void addRange(int model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour and model
+ */
+ Map<String, List<int[]>> modelData = atomSpec.get(model);
+ if (modelData == null)
+ {
+ atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
+ }
+
+ /*
+ * Get/initialize map of data for colour, model and chain
+ */
+ List<int[]> chainData = modelData.get(chain);
+ if (chainData == null)
+ {
+ chainData = new ArrayList<int[]>();
+ modelData.put(chain, chainData);
+ }
+
+ /*
+ * Add the start/end positions
+ */
+ chainData.add(new int[] { startPos, endPos });
+ // TODO add intelligently, using a RangeList class
+ }
+
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public String getAtomSpec()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.keySet())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+ final Map<String, List<int[]>> modelData = atomSpec.get(model);
+
+ for (String chain : modelData.keySet())
+ {
- chain = chain.trim();
++ // chain = chain.trim();
+
+ List<int[]> rangeList = modelData.get(chain);
+
+ /*
+ * sort ranges into ascending start position order
+ */
+ Collections.sort(rangeList, new RangeComparator(true));
+
+ int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
+ int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
+
+ Iterator<int[]> iterator = rangeList.iterator();
+ while (iterator.hasNext())
+ {
+ int[] range = iterator.next();
+ if (range[0] <= end + 1)
+ {
+ /*
+ * range overlaps or is contiguous with the last one
+ * - so just extend the end position, and carry on
+ * (unless this is the last in the list)
+ */
+ end = Math.max(end, range[1]);
+ }
+ else
+ {
+ /*
+ * we have a break so append the last range
+ */
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ start = range[0];
+ end = range[1];
+ }
+ }
+
+ /*
+ * and append the last range
+ */
+ if (!rangeList.isEmpty())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ protected void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+ if (chain.length() > 0)
+ {
+ sb.append(".").append(chain);
+ }
+ }
+ }
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+ import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
- import jalview.schemes.Blosum62ColourScheme;
- import jalview.schemes.BuriedColourScheme;
- import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
- import jalview.schemes.ColourSchemeProperty;
- import jalview.schemes.HelixColourScheme;
- import jalview.schemes.HydrophobicColourScheme;
- import jalview.schemes.NucleotideColourScheme;
- import jalview.schemes.PIDColourScheme;
- import jalview.schemes.PurinePyrimidineColourScheme;
- import jalview.schemes.RNAHelicesColourChooser;
+ import jalview.schemes.ColourSchemes;
+ import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
- import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
- import jalview.schemes.TaylorColourScheme;
- import jalview.schemes.TurnColourScheme;
- import jalview.schemes.UserColourScheme;
- import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
- import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
import java.io.File;
+ import java.io.FileWriter;
+ import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
- import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
- BLOSUM62Colour.setEnabled(false);
+ // BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
// PIDColour.setEnabled(false);
sortPairwiseMenuItem_actionPerformed(null);
}
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+ buildColourMenu();
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide();
+ }
if (viewport.getWrapAlignment())
{
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
- *
- * @param nucleotide
*/
- public void setGUINucleotide(boolean nucleotide)
+ public void setGUINucleotide()
{
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
+
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- nucleotideColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- RNAInteractionColour.setEnabled(nucleotide);
+
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ modifyPID.setEnabled(abovePIDThreshold.isSelected());
conservationMenuItem.setSelected(av.getConservationSelected());
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ ColourMenuHelper.setColourSelected(colourMenu,
+ av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
public void saveAs_actionPerformed(ActionEvent e)
{
String format = currentFileFormat == null ? null : currentFileFormat
- .toString();
+ .getName();
JalviewFileChooser chooser = JalviewFileChooser.forWrite(
Cache.getProperty("LAST_DIRECTORY"), format);
fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat.toString());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
Cache.setProperty("LAST_DIRECTORY", fileName);
saveAlignment(fileName, currentFileFormat);
}
else
{
- // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
- // {
- // warningMessage("Cannot save file " + fileName + " using format "
- // + format, "Alignment output format not supported");
- // if (!Jalview.isHeadlessMode())
- // {
- // saveAs_actionPerformed(null);
- // }
- // return false;
- // }
-
AlignmentExportData exportData = getAlignmentForExport(format,
viewport, null);
if (exportData.getSettings().isCancelled())
{
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ PrintWriter out = new PrintWriter(new FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[] { fileName, format }));
+ new Object[] { fileName, format.getName() }));
} catch (Exception ex)
{
success = false;
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
-
- FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
AlignmentExportData exportData = getAlignmentForExport(fileFormat,
viewport, null);
if (exportData.getSettings().isCancelled())
{
FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format,
- exportData.getAlignment(),
+ .formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(),
viewport.getColumnSelection()));
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
- seqs,
- omitHidden, null);
+ seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
/*
- * public void covariationColour_actionPerformed(ActionEvent e) {
+ * public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
new AnnotationColumnChooser(viewport, alignPanel);
}
+ /**
+ * Action on the user checking or unchecking the option to apply the selected
+ * colour scheme to all groups. If unchecked, groups may have their own
+ * independent colour schemes.
+ *
+ * @param selected
+ */
@Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void applyToAllGroups_actionPerformed(boolean selected)
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ viewport.setColourAppliesToAllGroups(selected);
}
/**
- * DOCUMENT ME!
+ * Action on user selecting a colour from the colour menu
*
- * @param e
- * DOCUMENT ME!
+ * @param name
+ * the name (not the menu item label!) of the colour scheme
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void changeColour_actionPerformed(String name)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel, null);
+ return;
+ }
+
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
+ changeColour(cs);
}
/**
- * DOCUMENT ME!
+ * Actions on setting or changing the alignment colour scheme
*
* @param cs
- * DOCUMENT ME!
*/
@Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
-
if (cs != null)
{
- // Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
+ ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
}
viewport.setGlobalColourScheme(cs);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the PID threshold slider panel
*/
@Override
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the Conservation slider panel
*/
@Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showConservationSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) By Conservation
*/
@Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
+ if (selected)
{
- new UserDefinedColours(alignPanel, null);
+ modifyConservation_actionPerformed();
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
+ SliderPanel.hideConservationSlider();
}
}
- public void updateUserColourMenu()
+ /**
+ * Action on selecting or deselecting (Colour) Above PID Threshold
+ */
+ @Override
+ public void abovePIDThreshold_actionPerformed(boolean selected)
{
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
+ changeColour(viewport.getGlobalColourScheme());
+ if (selected)
{
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
+ modifyPID_actionPerformed();
}
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ else
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
+ SliderPanel.hidePIDSlider();
}
}
* DOCUMENT ME!
*/
@Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
}
}
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
-
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ PDBEntry pe = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq((String) fm[0],
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
+ buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
}
if (FileFormat.Jnet.equals(format))
{
- JPredFile predictions = new JPredFile(
- file, sourceType);
+ JPredFile predictions = new JPredFile(file, sourceType);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
}
/*
+ * 'focus' any colour slider that is open to the selected viewport
+ */
+ if (viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
+ if (viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
+
+ /*
* If there is a frame linked to this one in a SplitPane, switch it to the
* same view tab index. No infinite recursion of calls should happen, since
* tabSelectionChanged() should not get invoked on setting the selected
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
true,
(actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
}
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ String schemeName = colourScheme == null ? null : colourScheme
+ .getSchemeName();
+
+ ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+ }
}
class PrintThread extends Thread
package jalview.gui;
import jalview.bin.Cache;
- import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
- import jalview.io.JalviewFileChooser;
- import jalview.io.JalviewFileView;
- import jalview.schemes.BuriedColourScheme;
- import jalview.schemes.ColourSchemeI;
- import jalview.schemes.HelixColourScheme;
- import jalview.schemes.HydrophobicColourScheme;
- import jalview.schemes.PurinePyrimidineColourScheme;
- import jalview.schemes.StrandColourScheme;
- import jalview.schemes.TaylorColourScheme;
- import jalview.schemes.TurnColourScheme;
- import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+ import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
- import java.awt.event.ItemEvent;
- import java.awt.event.ItemListener;
- import java.io.BufferedReader;
import java.io.File;
- import java.io.FileOutputStream;
- import java.io.FileReader;
- import java.io.IOException;
- import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
- import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
- import javax.swing.JMenu;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
- import javax.swing.event.MenuEvent;
- import javax.swing.event.MenuListener;
public class AppJmol extends StructureViewerBase
{
RenderPanel renderPanel;
- ViewSelectionMenu seqColourBy;
-
/**
*
* @param files
{
useAlignmentPanelForSuperposition(ap);
}
+ initMenus();
if (leaveColouringToJmol || !usetoColour)
{
jmb.setColourBySequence(false);
viewerColour.setSelected(false);
}
this.setBounds(bounds);
- initMenus();
setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
closeViewer(false);
}
});
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!ˇ
+
}
- private void initMenus()
+ @Override
+ protected void initMenus()
{
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new String[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ super.initMenus();
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ viewerActionMenu.setText(MessageManager.getString("label.jmol"));
- }
- });
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
IProgressIndicator progressBar = null;
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
/**
* add a single PDB structure to a new or existing Jmol view
*
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
- /**
- * Answers true if this viewer already involves the given PDB ID
- */
- @Override
- protected boolean hasPdbId(String pdbId)
- {
- return jmb.hasPdbId(pdbId);
- }
-
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- }
-
- @Override
public void eps_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
{
getSize(currentSize);
- if (jmb != null && jmb.fileLoadingError != null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.getChainNames());
-
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
- }
-
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return getAlignmentPanel();
- }
-
@Override
public AAStructureBindingModel getBinding()
{
}
@Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
++
++ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
-
}
package jalview.gui;
import jalview.bin.Cache;
- import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
- import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+ import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
- import jalview.io.JalviewFileChooser;
- import jalview.io.JalviewFileView;
import jalview.io.StructureFile;
- import jalview.schemes.BuriedColourScheme;
- import jalview.schemes.ColourSchemeI;
- import jalview.schemes.HelixColourScheme;
- import jalview.schemes.HydrophobicColourScheme;
- import jalview.schemes.PurinePyrimidineColourScheme;
- import jalview.schemes.StrandColourScheme;
- import jalview.schemes.TaylorColourScheme;
- import jalview.schemes.TurnColourScheme;
- import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+ import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
import java.awt.event.ActionEvent;
- import java.awt.event.ItemEvent;
- import java.awt.event.ItemListener;
- import java.io.BufferedReader;
+ import java.awt.event.ActionListener;
+ import java.awt.event.MouseAdapter;
+ import java.awt.event.MouseEvent;
import java.io.File;
import java.io.FileInputStream;
- import java.io.FileOutputStream;
- import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
- import java.io.PrintWriter;
import java.util.ArrayList;
+ import java.util.Collections;
import java.util.List;
import java.util.Random;
- import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
- import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
+ import javax.swing.JMenuItem;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
- import javax.swing.event.MenuEvent;
- import javax.swing.event.MenuListener;
/**
* GUI elements for handling an external chimera display
{
private JalviewChimeraBinding jmb;
- private boolean allChainsSelected = false;
-
private IProgressIndicator progressBar = null;
/*
private Random random = new Random();
+ private int myWidth = 500;
+
+ private int myHeight = 150;
+
/**
* Initialise menu options.
*/
- private void initMenus()
+ @Override
+ protected void initMenus()
{
+ super.initMenus();
+
viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+
viewerColour.setText(MessageManager
.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
.getString("label.let_chimera_manage_structure_colours"));
- helpItem.setText(MessageManager.getString("label.chimera_help"));
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- // save As not yet implemented
- savemenu.setVisible(false);
- ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the Chimera display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
+ helpItem.setText(MessageManager.getString("label.chimera_help"));
+ savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new Object[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
{
-
@Override
- public void menuSelected(MenuEvent e)
+ public void actionPerformed(ActionEvent e)
{
- handler.itemStateChanged(null);
+ sendFeaturesToChimera();
}
+ });
+ viewerActionMenu.add(writeFeatures);
+
+ final JMenu fetchAttributes = new JMenu(
+ MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes.setToolTipText(MessageManager
+ .getString("label.fetch_chimera_attributes_tip"));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
@Override
- public void menuDeselected(MenuEvent e)
+ public void mouseEntered(MouseEvent e)
{
- // TODO Auto-generated method stub
+ buildAttributesMenu(fetchAttributes);
}
+ });
+ viewerActionMenu.add(fetchAttributes);
- @Override
- public void menuCanceled(MenuEvent e)
+ }
+
+ /**
+ * Query Chimera for its residue attribute names and add them as items off the
+ * attributes menu
+ *
+ * @param attributesMenu
+ */
+ protected void buildAttributesMenu(JMenu attributesMenu)
+ {
+ List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+ if (atts == null)
+ {
+ return;
+ }
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (String att : atts)
+ {
+ final String attName = att.split(" ")[1];
+
+ /*
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- // TODO Auto-generated method stub
+ JMenuItem menuItem = new JMenuItem(attName);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getChimeraAttributes(attName);
+ }
+ });
+ attributesMenu.add(menuItem);
}
- });
+ }
+ }
+
+ /**
+ * Read residues in Chimera with the given attribute name, and set as features
+ * on the corresponding sequence positions (if any)
+ *
+ * @param attName
+ */
+ protected void getChimeraAttributes(String attName)
+ {
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+ }
+
+ /**
+ * Send a command to Chimera to create residue attributes for Jalview features
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ */
+ protected void sendFeaturesToChimera()
+ {
+ int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
+ statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+ count));
}
/**
}
}
- /**
- * Answers true if this viewer already involves the given PDB ID
- */
- @Override
- protected boolean hasPdbId(String pdbId)
- {
- return jmb.hasPdbId(pdbId);
- }
-
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
createProgressBar();
- // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
jmb.setColourBySequence(true);
- setSize(400, 400); // probably should be a configurable/dynamic default here
+ setSize(myWidth, myHeight);
initMenus();
addingStructures = false;
}
-
-
/**
* Create a new viewer from saved session state data including Chimera session
* file
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this,
- jmb.getViewerTitle("Chimera", true), getBounds().width,
+ Desktop.addInternalFrame(this,
+ jmb.getViewerTitle(getViewerName(), true), getBounds().width,
getBounds().height);
if (!jmb.launchChimera())
+ chimeraSessionFile);
}
}
- jmb.setFinishedInit(true);
jmb.startChimeraListener();
}
-
/**
* Show only the selected chain(s) in the viewer
*/
{
String prompt = MessageManager.formatMessage(
"label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle("Chimera", false) });
+ new Object[] { jmb.getViewerTitle(getViewerName(),
+ false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
if (files.length() > 0)
{
+ jmb.setFinishedInit(false);
if (!addingStructures)
{
try
try
{
int pos = filePDBpos.get(num).intValue();
- long startTime = startProgressBar("Chimera "
+ long startTime = startProgressBar(getViewerName() + " "
+ MessageManager.getString("status.opening_file_for")
+ " " + pe.getId());
jmb.openFile(pe);
}
// Explicitly map to the filename used by Chimera ;
pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos], pe.getFile(), protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ progressBar);
stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
}
}
}
+
jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @return
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- e.printStackTrace();
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- }
-
- @Override
public void eps_actionPerformed(ActionEvent e)
{
throw new Error(
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
- } catch (Exception ex)
- {
- }
- }
-
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.getChainNames());
-
- this.setTitle(jmb.getViewerTitle("Chimera", true));
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
-
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
-
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
- }
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
+ } catch (IOException ex)
{
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
}
- return getAlignmentPanel();
}
@Override
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Chimera";
+ }
+
+ /**
+ * Sends commands to align structures according to associated alignment(s).
+ *
+ * @return
+ */
+ @Override
+ protected String alignStructs_withAllAlignPanels()
+ {
+ String reply = super.alignStructs_withAllAlignPanels();
+ if (reply != null)
+ {
+ statusBar.setText("Superposition failed: " + reply);
+ }
+ return reply;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
++
++ @Override
++ protected AAStructureBindingModel getBindingModel()
++ {
++ return jmb;
++ }
}
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+ import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
// group has references so set its ID field
jGroup.setId(groupRefs.get(sg));
}
- if (sg.cs != null)
+ ColourSchemeI colourScheme = sg.getColourScheme();
+ if (colourScheme != null)
{
- if (sg.cs.conservationApplied())
+ ResidueShaderI groupColourScheme = sg
+ .getGroupColourScheme();
+ if (groupColourScheme.conservationApplied())
{
- jGroup.setConsThreshold(sg.cs.getConservationInc());
+ jGroup.setConsThreshold(groupColourScheme.getConservationInc());
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
}
- else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+ else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
{
jGroup.setColour("AnnotationColourGradient");
jGroup.setAnnotationColours(constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) sg.cs,
+ (jalview.schemes.AnnotationColourGradient) colourScheme,
userColours, jms));
}
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ else if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
- jGroup.setPidThreshold(sg.cs.getThreshold());
+ jGroup.setPidThreshold(groupColourScheme.getThreshold());
}
jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
.getGlobalColourScheme()));
}
+ ResidueShaderI vcs = av.getResidueShading();
ColourSchemeI cs = av.getGlobalColourScheme();
if (cs != null)
{
- if (cs.conservationApplied())
+ if (vcs.conservationApplied())
{
- view.setConsThreshold(cs.getConservationInc());
+ view.setConsThreshold(vcs.getConservationInc());
if (cs instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(cs, userColours, jms));
}
}
-
- if (cs instanceof ResidueColourScheme)
- {
- view.setPidThreshold(cs.getThreshold());
- }
+ view.setPidThreshold(vcs.getThreshold());
}
view.setConservationSelected(av.getConservationSelected());
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
&& jGroup.getAnnotationColours() != null)
{
addAnnotSchemeGroup = true;
}
else
{
- cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(jGroup.getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
}
}
+ int pidThreshold = jGroup.getPidThreshold();
Vector<SequenceI> seqs = new Vector<SequenceI>();
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
-
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
sg.textColour = new java.awt.Color(jGroup.getTextCol1());
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
- null, al, jms, false);
+ sg.setColourScheme(constructAnnotationColour(
+ jGroup.getAnnotationColours(), null, al, jms, false));
}
}
}
StructureData filedat = oldFiles.get(id);
String pdbFile = filedat.getFilePath();
SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
- binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
+ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+ null);
binding.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the view panel
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setThreshold(view.getPidThreshold());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
}
af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getResidueShading().setThreshold(
+ view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setConsensus(
+ af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
{
- cs.setConservationInc(view.getConsThreshold());
+ af.viewport.getResidueShading().setConservationInc(
+ view.getConsThreshold());
}
af.changeColour(cs);
propagateAnnColour = true;
for (jalview.datamodel.SequenceGroup sg : al.getGroups())
{
- if (sg.cs instanceof AnnotationColourGradient)
+ if (sg.getColourScheme() instanceof AnnotationColourGradient)
{
propagateAnnColour = false;
}
);
}
- if (viewAnnColour.getColourScheme().equals("None"))
+ if (viewAnnColour.getColourScheme().equals(
+ ResidueColourScheme.NONE))
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
+ ColourSchemeProperty.getColourScheme(al,
viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}
}
/*
- * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
* new AnnotationColourGradient(
* annAlignment.getAlignmentAnnotation()[i], new
* java.awt.Color(viewAnnColour. getMinColour()), new
* viewAnnColour.getAboveThreshold()); } else
*/
{
- sg.cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i], sg.cs,
- viewAnnColour.getAboveThreshold());
+ sg.setColourScheme(new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i], sg
+ .getColourScheme(), viewAnnColour
+ .getAboveThreshold()));
if (cs instanceof AnnotationColourGradient)
{
if (viewAnnColour.hasPerSequence())
*/
package jalview.gui;
+ import jalview.bin.Cache;
+ import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.DataSourceType;
+ import jalview.io.JalviewFileChooser;
+ import jalview.io.JalviewFileView;
import jalview.jbgui.GStructureViewer;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemes;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+ import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+ import java.io.BufferedReader;
+ import java.io.File;
+ import java.io.FileOutputStream;
+ import java.io.FileReader;
+ import java.io.IOException;
+ import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
+ import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
+ import javax.swing.JColorChooser;
+ import javax.swing.JMenu;
import javax.swing.JMenuItem;
+ import javax.swing.JRadioButtonMenuItem;
+ import javax.swing.event.MenuEvent;
+ import javax.swing.event.MenuListener;
/**
* Base class with common functionality for JMol, Chimera or other structure
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ /*
+ * names for colour options (additional to Jalview colour schemes)
+ */
+ enum ViewerColour
+ {
+ BySequence, ByChain, ChargeCysteine, ByViewer
+ }
/**
* list of sequenceSet ids associated with the view
protected boolean allChainsSelected = false;
+ protected JMenu viewSelectionMenu;
+
+ /**
+ * Default constructor
+ */
+ public StructureViewerBase()
+ {
+ super();
+ }
/**
*
* @param ap2
public abstract ViewerType getViewerType();
+ protected abstract AAStructureBindingModel getBindingModel();
+
+ protected abstract IProgressIndicator getIProgressIndicator();
+
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
}
}
// otherwise, start adding the structure.
- getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry },
+ getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
new SequenceI[][] { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
return option;
}
- protected abstract boolean hasPdbId(String pdbId);
+ protected boolean hasPdbId(String pdbId)
+ {
+ return getBinding().hasPdbId(pdbId);
+ }
protected abstract List<StructureViewerBase> getViewersFor(
AlignmentPanel alp);
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE);
+ pdbFilename, DataSourceType.FILE, getIProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
// JBPNOTE: this looks like a binding routine, rather than a gui routine
for (StructureViewerBase viewer : getViewersFor(null))
{
- AAStructureBindingModel bindingModel = viewer.getBindingModel();
+ AAStructureBindingModel bindingModel = viewer.getBinding();
for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
{
if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
abstract void showSelectedChains();
+ /**
+ * Action on selecting one of Jalview's registered colour schemes
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
+ colourSchemeName, al, null);
+ getBinding().setJalviewColourScheme(cs);
+ }
+
+ /**
+ * Builds the colour menu
+ */
+ protected void buildColourMenu()
+ {
+ colourMenu.removeAll();
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+
+ /*
+ * add colour by sequence, by chain, by charge and cysteine
+ */
+ colourMenu.add(seqColour);
+ colourMenu.add(chainColour);
+ colourMenu.add(chargeColour);
+ chargeColour.setEnabled(!al.isNucleotide());
+
+ /*
+ * add all 'simple' (per-residue) colour schemes registered to Jalview
+ */
+ ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
+ al, true);
+
+ /*
+ * add 'colour by viewer' (menu item text is set in subclasses)
+ */
+ viewerColour.setSelected(false);
+ viewerColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewerColour_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(viewerColour);
+
+ /*
+ * add 'set background colour'
+ */
+ JMenuItem backGround = new JMenuItem();
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
+ backGround.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ background_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(backGround);
+
+ /*
+ * add colour buttons to a group so their selection is
+ * mutually exclusive (background colour is a separate option)
+ */
+ itemGroup.add(seqColour);
+ itemGroup.add(chainColour);
+ itemGroup.add(chargeColour);
+ itemGroup.add(viewerColour);
+ }
+
+ /**
+ * Construct menu items
+ */
+ protected void initMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+
+ seqColour = new JRadioButtonMenuItem();
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
+ seqColour.setName(ViewerColour.BySequence.name());
+ seqColour.setSelected(binding.isColourBySequence());
+ seqColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ seqColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chainColour = new JRadioButtonMenuItem();
+ chainColour.setText(MessageManager.getString("action.by_chain"));
+ chainColour.setName(ViewerColour.ByChain.name());
+ chainColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chargeColour = new JRadioButtonMenuItem();
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
+ chargeColour.setName(ViewerColour.ChargeCysteine.name());
+ chargeColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour_actionPerformed(actionEvent);
+ }
+ });
+
+ viewerColour = new JRadioButtonMenuItem();
+ // text is set in overrides of this method
+ viewerColour.setName(ViewerColour.ByViewer.name());
+ viewerColour.setSelected(!binding.isColourBySequence());
+
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the Chimera display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+
+ final ItemListener handler = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(!_alignwith.isEmpty());
+ alignStructs.setToolTipText(MessageManager.formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ _alignwith.size()));
+ }
+ };
+ viewSelectionMenu = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
+ _alignwith, handler);
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(viewSelectionMenu, 0);
+ viewerActionMenu.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+
+ buildColourMenu();
+ }
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs) {
+ getBinding().setJalviewColourScheme(cs);
+ }
+
+ /**
+ * Sends commands to the structure viewer to superimpose structures based on
+ * currently associated alignments. May optionally return an error message for
+ * the operation.
+ */
+ @Override
+ protected String alignStructs_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ return alignStructs_withAllAlignPanels();
+ }
+
+ protected String alignStructs_withAllAlignPanels()
+ {
+ if (getAlignmentPanel() == null)
+ {
+ return null;
+ }
+
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(getAlignmentPanel());
+ }
+
+ String reply = null;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ reply = getBinding().superposeStructures(als, alm, alc);
+ if (reply != null)
+ {
+ String text = MessageManager.formatMessage(
+ "error.superposition_failed", reply);
+ statusBar.setText(text);
+ }
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+ }
+ return reply;
+ }
+
+ @Override
+ public void background_actionPerformed(ActionEvent actionEvent)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
+ null);
+ if (col != null)
+ {
+ getBinding().setBackgroundColour(col);
+ }
+ }
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ getBinding().setColourBySequence(false);
+ }
+ }
+ @Override
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ getBinding().colourByChain();
+ }
+ @Override
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ getBinding().colourByCharge();
+ }
+ @Override
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+ AAStructureBindingModel binding = getBinding();
+ binding.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (binding.isColourBySequence())
+ {
+ if (!binding.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ binding.colourBySequence(ap);
+ }
+ }
+ }
+ @Override
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ BufferedReader in = null;
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ in = new BufferedReader(
+ new FileReader(getBinding().getPdbFile()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+ }
+ @Override
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.appendText(getBinding().printMappings());
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ protected abstract String getViewerName();
+
+ /**
+ * Configures the title and menu items of the viewer panel.
+ */
+ public void updateTitleAndMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding.hasFileLoadingError())
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(binding.getChainNames());
+
+ this.setTitle(binding.getViewerTitle(getViewerName(), true));
+
+ /*
+ * enable 'Superpose with' if more than one mapped structure
+ */
+ viewSelectionMenu.setEnabled(false);
+ if (getBinding().getPdbFile().length > 1
+ && getBinding().getSequence().length > 1)
+ {
+ viewSelectionMenu.setEnabled(true);
+ }
+
+ /*
+ * Show action menu if it has any enabled items
+ */
+ viewerActionMenu.setVisible(false);
+ for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
+ {
+ if (viewerActionMenu.getItem(i).isEnabled())
+ {
+ viewerActionMenu.setVisible(true);
+ break;
+ }
+ }
+
+ if (!binding.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
}
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
- import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
+ import jalview.util.ColorUtils;
+ import java.awt.Color;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.io.StringReader;
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(sg.cs.toString());
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
String file, DataSourceType sourceType)
{
+ baseUri = "";
BufferedReader in = null;
try
{
if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
+ baseUri = new File(file).getParent();
+ if (baseUri == null)
+ {
+ baseUri = "";
+ }
+ else
+ {
+ baseUri += "/";
+ }
}
else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String bs = url.toExternalForm();
+ baseUri = bs.substring(0, bs.indexOf(url.getHost())
+ + url.getHost().length());
+ baseUri += url.toURI().getPath();
+ if (baseUri.lastIndexOf("/") > -1)
+ {
+ baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
+ }
}
else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
+ // TODO - support mimencoded PDBs for a paste.. ?
+ baseUri = "";
}
else if (sourceType == DataSourceType.CLASSLOADER)
{
if (is != null)
{
in = new BufferedReader(new java.io.InputStreamReader(is));
+ // TODO: this probably doesn't work for classloader - needs a test
+ baseUri = new File("/" + file).getParent() + "/";
}
}
if (in != null)
String lastread = "";
- private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
BufferedReader in) throws Exception
modified = true;
continue;
}
-
+ else if (token.equalsIgnoreCase(STRUCTMODEL))
+ {
+ boolean failedtoadd = true;
+ // expect
+ // STRUCTMODEL <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile>
+ // <Confidence> <%.I.D>
+ // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
+ String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
+ SequenceI querySeq = al.findName(querySeqId);
+ if (st.hasMoreTokens()) {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ System.err.println("Couldn't locate " + refSeqId
+ + " in the alignment for STRUCTMODEL");
+ refSeqId = null;
+ }
+ else
+ {
+ String tempId = st.nextToken();
+ String fastaMapping = st.nextToken();
+ String confidence = !st.hasMoreTokens() ? "" : 100
+ * Double.valueOf(st.nextToken()) + "";
+ String pid = !st.hasMoreTokens() ? "" : st.nextToken();
+ String alignRange = !st.hasMoreTokens() ? "" : st.nextToken()
+ + "-" + st.nextToken();
+ String otherInfo = !st.hasMoreTokens() ? "" : st.nextToken();
+ String coverage = "";
+ if (add_structmodel(al, querySeq, refSeq, tempId,
+ fastaMapping,
+ alignRange, coverage,
+ confidence, pid, otherInfo))
+ {
+ failedtoadd = false;
+ }
+ }
+ }
+ if (failedtoadd)
+ {
+ System.err
+ .println("Need <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ + STRUCTMODEL
+ + ".\nNote: other information could be provided in html format ");
+ } else {
+ modified = true;
+ }
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
return modified;
}
+ /**
+ * resolve a structural model and generate and add an alignment sequence for
+ * it
+ *
+ * @param refSeq2
+ * @param tempId
+ * @param urlToModel
+ * @param urlToPairwise
+ * @return true if model and sequence was added
+ */
+ private boolean add_structmodel(AlignmentI al, SequenceI querySequence,
+ SequenceI templateSeq,
+ String modelFile, String fastaFile, String aRange,
+ String coverage, String confidence,
+ String pid, String otherInfo)
+ {
+ String warningMessage = null;
+ boolean added = false;
+ try {
+ String structureModelFile = resolveAbsolute(modelFile);
+ String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
+ ".fasta.jal", ".fasta"));
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ structureModelFile);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
+ coverage, confidence, pid, otherInfo);
+ phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
+ added = true;
+
+ } catch (Exception x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ }
+ return added;
+ }
+
+ private String generatePhyre2InfoHTMLTable(String aRange,
+ String coverage, String confidence, String pid, String otherInfo)
+ {
+ StringBuilder phyre2InfoBuilder = new StringBuilder();
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>");
+ phyre2InfoBuilder
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ if (aRange != null && !aRange.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Aligned range")
+ .append("</td><td>").append(aRange).append("</td></tr>");
+ }
+ if (coverage != null && !coverage.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Coverage")
+ .append("</td><td>").append(coverage).append("</td></tr>");
+ }
+ if (confidence != null && !confidence.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Confidence")
+ .append("</td><td>").append(confidence).append("</td></tr>");
+ }
+ if (pid != null && !pid.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
+ .append("</td><td>").append(pid).append("</td></tr>");
+ }
+ if (otherInfo != null && !otherInfo.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Other information")
+ .append("</td><td>").append(otherInfo).append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ return phyre2InfoBuilder.toString();
+ }
+
+ private String resolveAbsolute(String relURI)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(baseUri) || relURI.startsWith(baseUri))
+ {
+ return relURI;
+ }
+ return baseUri + relURI;
+ }
+
private void parseHideCols(ColumnSelection colSel, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
Annotation parseAnnotation(String string, int graphStyle)
{
- boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
- // do the
- // glyph
- // test
- // if we
- // don't
- // want
- // secondary
- // structure
+ // don't do the glyph test if we don't want secondary structure
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
- java.awt.Color colour = null;
+ Color colour = null;
int i = string.indexOf("[");
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
- UserColourScheme ucs = new UserColourScheme();
-
- colour = ucs.getColourFromString(string.substring(i + 1, j));
+ colour = ColorUtils.parseColourString(string.substring(i + 1,
+ j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
void colourAnnotations(AlignmentI al, String label, String colour)
{
- UserColourScheme ucs = new UserColourScheme(colour);
+ Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
{
if (annotations[j] != null)
{
- annotations[j].colour = ucs.findColour('A');
+ annotations[j].colour = awtColour;
}
}
}
SequenceGroup groupRef)
{
String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- float value = new Float(st.nextToken()).floatValue();
+ AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+ String nextToken = st.nextToken();
+ float value = 0f;
+ try
+ {
+ value = Float.valueOf(nextToken);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ + "' invalid, setting to zero");
+ }
String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
+ Color colour = null;
if (st.hasMoreTokens())
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
+ colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
}
}
}
- if (annotation == null)
- {
- return;
- }
}
void addGroup(AlignmentI al, StringTokenizer st)
if (sg != null)
{
String keyValue, key, value;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
+ ColourSchemeI def = sg.getColourScheme();
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs.setColourScheme(ColourSchemeProperty
+ .getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
}
else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
}
sg.recalcConservation();
}
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
- sg.cs = def;
+ sg.setColourScheme(def);
}
}
}
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.ws.phyre2.Phyre2Client;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
private long progressSessionId;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+ private Map<String, String> phyre2ModelTemplates = new Hashtable<String, String>();
+
/**
* @return true if will try to use external services for processing secondary
* structure
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol)
+ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
- return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress);
}
+
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* - one or more sequences to be mapped to pdbFile
* @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
+ * (may be null, individual elements may be null)
* @param pdbFile
* - structure data resource
- * @param sourceType
+ * @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
+ String pdbFile, DataSourceType protocol)
{
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, protocol, null);
+ }
+
+ synchronized public StructureFile computeMapping(
+ boolean forStructureView, SequenceI[] sequenceArray,
+ String[] targetChainIds, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
+ {
+ long progressSessionId = System.currentTimeMillis() * 3;
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new JmolParser(pdbFile, sourceType);
+ pdb = new JmolParser(pdbFile, protocol);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && DataSourceType.FILE == sourceType)
+ && DataSourceType.FILE == protocol)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
continue;
}
- if (sourceType == DataSourceType.PASTE)
+ if (protocol.equals(DataSourceType.PASTE))
{
pdbFile = "INLINE" + pdb.getId();
}
-
+ boolean phyre2Template = isPhyre2Template(pdbFile);
List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs && seq.isProtein())
+ if (!phyre2Template && isMapUsingSIFTs && seq.isProtein())
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
+ if (progress!=null) {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
+ }
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
else
} catch (SiftsException e)
{
System.err.println(e.getMessage());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
if (!foundSiftsMappings.isEmpty())
}
}
}
- else
+ else if (phyre2Template)
{
setProgressBar(null);
setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
+ .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+ String fastaFile = getPhyre2FastaFileFor(pdbFile);
+ StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+ .getStructureMapping(seq, pdbFile, fastaFile, " ");
+ seqToStrucMapping.add(phyre2ModelMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
+ else
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
return pdb;
}
- public void addStructureMapping(StructureMapping sm)
+ public void registerPhyre2Template(String phyre2Template,
+ String fastaMappingFile)
{
- mappings.add(sm);
+ phyre2ModelTemplates.put(phyre2Template, fastaMappingFile);
}
/**
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
+ AlignSeq maxAlignseq) throws Exception
{
StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ .getStructureMapping(seq, pdbFile, targetChainId);
try
{
PDBChain chain = pdb.findChain(targetChainId);
return;
}
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(results);
+ }
+ }
+ }
+
+ /**
+ * Constructs a SearchResults object holding regions (if any) in the Jalview
+ * alignment which have a mapping to the structure viewer positions in the
+ * supplied list
+ *
+ * @param atoms
+ * @return
+ */
+ public SearchResultsI findAlignmentPositionsForStructurePositions(
+ List<AtomSpec> atoms)
+ {
SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
}
}
}
- for (Object li : listeners)
- {
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
- }
+ return results;
}
/**
return seqmappings;
}
+ public boolean isPhyre2Template(String structureFile)
+ {
+ if (structureFile == null || phyre2ModelTemplates == null
+ || phyre2ModelTemplates.isEmpty())
+ {
+ return false;
+ }
+ return phyre2ModelTemplates.get(structureFile) != null
+ && !phyre2ModelTemplates.get(structureFile).isEmpty();
+ }
+
+ public String getPhyre2FastaFileFor(String structureFile)
+ {
+ return phyre2ModelTemplates.get(structureFile);
+ }
+
+
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
++ public void addStructureMapping(StructureMapping smapping)
++ {
++ mappings.add(smapping);
++ }
++
}
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingClient;
+import jalview.structures.models.MappingOutputModel;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.Format;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import MCview.Atom;
-import MCview.PDBChain;
-
-public class SiftsClient implements SiftsClientI
+public class SiftsClient extends StructureMappingClient implements
+ SiftsClientI
{
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
private Entry siftsEntry;
- private StructureFile pdb;
-
private String pdbId;
private String structId;
private static final int PDB_RES_POS = 0;
- private static final int PDB_ATOM_POS = 1;
-
private static final String NOT_OBSERVED = "Not_Observed";
private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
* @param pdbId
* @throws SiftsException
*/
- public SiftsClient(StructureFile pdb) throws SiftsException
+ public SiftsClient(StructureFile structureFile) throws SiftsException
{
- this.pdb = pdb;
- this.pdbId = pdb.getId();
+ this.structureFile = structureFile;
+ this.pdbId = structureFile.getId();
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
+ /*
+ * return mocked file if it has been set
+ */
+ if (mockSiftsFile != null)
+ {
+ return mockSiftsFile;
+ }
+
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ pdbId.toLowerCase() + ".xml.gz";
File siftsFile = new File(siftsFileName);
}
@Override
- public StructureMapping getSiftsStructureMapping(SequenceI seq,
- String pdbFile, String chain) throws SiftsException
+ public StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String chain) throws Exception,
+ StructureMappingException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
System.out.println("Getting SIFTS mapping for " + structId + ": seq "
@Override
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
- SequenceI seq, java.io.PrintStream os) throws SiftsException
+ SequenceI seq, java.io.PrintStream os) throws SiftsException,
+ StructureMappingException
{
List<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
if (os != null)
{
- MappingOutputPojo mop = new MappingOutputPojo();
+ MappingOutputModel mop = new MappingOutputModel();
mop.setSeqStart(seqStart);
mop.setSeqEnd(seqEnd);
mop.setSeqName(seq.getName());
}
}
- /**
- *
- * @param chainId
- * Target chain to populate mapping of its atom positions.
- * @param mapping
- * Two dimension array of residue index versus atom position
- * @throws IllegalArgumentException
- * Thrown if chainId or mapping is null
- * @throws SiftsException
- */
- void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)
- throws IllegalArgumentException, SiftsException
- {
- try
- {
- PDBChain chain = pdb.findChain(chainId);
-
- if (chain == null || mapping == null)
- {
- throw new IllegalArgumentException(
- "Chain id or mapping must not be null.");
- }
- for (int[] map : mapping.values())
- {
- if (map[PDB_RES_POS] != UNASSIGNED)
- {
- map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
- }
- }
- } catch (NullPointerException e)
- {
- throw new SiftsException(e.getMessage());
- } catch (Exception e)
- {
- throw new SiftsException(e.getMessage());
- }
- }
-
- /**
- *
- * @param residueIndex
- * The residue index used for the search
- * @param atoms
- * A collection of Atom to search
- * @return atom position for the given residue index
- */
- int getAtomIndex(int residueIndex, Collection<Atom> atoms)
- {
- if (atoms == null)
- {
- throw new IllegalArgumentException(
- "atoms collection must not be null!");
- }
- for (Atom atom : atoms)
- {
- if (atom.resNumber == residueIndex)
- {
- return atom.atomIndex;
- }
- }
- return UNASSIGNED;
- }
/**
* Checks if the residue instance is marked 'Not_observed' or not
}
@Override
- public StringBuffer getMappingOutput(MappingOutputPojo mp)
- throws SiftsException
+ public StringBuffer getMappingOutput(MappingOutputModel mp)
+ throws StructureMappingException
{
String seqRes = mp.getSeqResidue();
String seqName = mp.getSeqName();
float pid = (float) matchedSeqCount / seqRes.length() * 100;
if (pid < SiftsSettings.getFailSafePIDThreshold())
{
- throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
+ throw new StructureMappingException(
+ ">>> Low PID detected for SIFTs mapping...");
}
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
return siftsEntry.getDbVersion();
}
+ public static void setMockSiftsFile(File file)
+ {
+ mockSiftsFile = file;
+ }
+
}
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+ import jalview.api.AlignViewportI;
+ import jalview.api.AlignmentViewPanel;
+ import jalview.api.FeatureRenderer;
+ import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
+ import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
+ import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
+ import java.awt.Color;
import java.util.Arrays;
+ import java.util.BitSet;
import java.util.List;
import org.testng.annotations.BeforeClass;
StructureSelectionManager ssm = new StructureSelectionManager();
ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
+
testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
{
{
return null;
}
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ }
+
+ @Override
+ public String superposeStructures(AlignmentI[] als, int[] alm,
+ ColumnSelection[] alc)
+ {
+ return null;
+ }
+
+ @Override
+ public void setBackgroundColour(Color col)
+ {
+ }
+
+ @Override
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignViewportI viewport)
+ {
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
+ {
+ }
+
+ @Override
+ public void colourByChain()
+ {
+ }
+
+ @Override
+ public void colourByCharge()
+ {
+ }
};
}
structs[i] = testee.new SuperposeData(al.getWidth());
}
/*
- * initialise array of 'superposable columns' to true (would be false for
+ * initialise BitSet of 'superposable columns' to true (would be false for
* hidden columns)
*/
- boolean[] matched = new boolean[al.getWidth()];
- Arrays.fill(matched, true);
+ BitSet matched = new BitSet();
+ for (int i = 0; i < al.getWidth(); i++)
+ {
+ matched.set(i);
+ }
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
/*
* only ungapped, structure-mapped columns are superposable
*/
- assertFalse(matched[0]); // gap in first sequence
- assertTrue(matched[1]);
- assertFalse(matched[2]); // gap in third sequence
- assertFalse(matched[3]); // gap in fourth sequence
- assertTrue(matched[4]);
- assertTrue(matched[5]); // gap in second sequence
+ assertFalse(matched.get(0)); // gap in first sequence
+ assertTrue(matched.get(1));
+ assertFalse(matched.get(2)); // gap in third sequence
+ assertFalse(matched.get(3)); // gap in fourth sequence
+ assertTrue(matched.get(4));
+ assertTrue(matched.get(5)); // gap in second sequence
assertEquals("1YCS", structs[0].pdbId);
assertEquals("3A6S", structs[1].pdbId);
structs[i] = testee.new SuperposeData(al.getWidth());
}
/*
- * initialise array of 'superposable columns' to true (would be false for
+ * initialise BitSet of 'superposable columns' to true (would be false for
* hidden columns)
*/
- boolean[] matched = new boolean[al.getWidth()];
- Arrays.fill(matched, true);
+ BitSet matched = new BitSet();
+ for (int i = 0; i < al.getWidth(); i++)
+ {
+ matched.set(i);
+ }
+
// treat column 5 of the alignment as hidden
- matched[4] = false;
+ matched.clear(4);
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
assertEquals(0, refStructure);
// only ungapped, structure-mapped columns are not superposable
- assertFalse(matched[0]);
- assertTrue(matched[1]);
- assertFalse(matched[2]);
- assertFalse(matched[3]);
- assertFalse(matched[4]); // superposable, but hidden, column
- assertTrue(matched[5]);
+ assertFalse(matched.get(0));
+ assertTrue(matched.get(1));
+ assertFalse(matched.get(2));
+ assertFalse(matched.get(3));
+ assertFalse(matched.get(4)); // superposable, but hidden, column
+ assertTrue(matched.get(5));
}
}
git://source.jalview.org / jalview.git / commitdiff