Preferences

From: Jim Procter Date: Tue, 4 Jun 2019 17:22:21 +0000 (+0100) Subject: Merge branch 'develop' into developtomchmmer X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b5667f39acdf309cd92881b73edfda591e0acaf4;p=jalview.git Merge branch 'develop' into developtomchmmer JAL-3285 merged 2.11 develop into the features/mchmmer branch - need to fix code for migration from Castor to JAXB - need to check Stockholm file IO and tests Good luck ! --- b5667f39acdf309cd92881b73edfda591e0acaf4 diff --cc help/help/help.jhm index 0000000,1666cc6..8ffef1e mode 000000,100755..100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@@ -1,0 -1,168 +1,169 @@@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --cc help/help/helpTOC.xml index 0000000,77ddd88..0bf615b mode 000000,100755..100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@@ -1,0 -1,175 +1,176 @@@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + diff --cc help/help/html/features/preferences.html index 0000000,8c6b699..5bb0b8a mode 000000,100755..100755 --- a/help/help/html/features/preferences.html +++ b/help/help/html/features/preferences.html @@@ -1,0 -1,388 +1,397 @@@ + + + + Preferences + + + +

+ Preferences +

+ The preferences panel is opened from the Jalview Desktop’s Tools + menu. +

There are eight tabs in the Preferences dialog box: +

The "Visual" + Preferences tab allows you to configure the default display for + a new alignment window. +
The "Colours" + Preferences tab allows you to configure default colourschemes + for a new alignment window. +
The "Overview" + Preferences tab configures defaults for the overview window. +
The "Structure" + Preferences tab allows you to configure options for obtaining + and displaying structure information. +
The "Connections" + Preferences tab allows you to configure Jalview's internet + settings and specify your default web browser. +
The "Links" + Preferences tab shows the currently configured URL + Links shown in the Link submenu in the Sequence + ID popup menu. +
The "Output" + Preferences tab contains settings affecting the export of + sequence alignments and EPS files. +
The "Editing" + Preferences tab contains settings affecting behaviour when editing alignments. +
The "HMMER" ++ Preferences tab allows you to configure locally installed HMMER tools. ++
The "Web + Service" Preferences tab allows you to configure the JABAWS + servers that Jalview uses, and change the layout of the + alignment's Web Services menu. +

+ Visual Preferences tab +

+ Maximise Window - If this is selected, a new alignment + window will stretch to fit the available space. +

+ Open Overview Window - When this is selected, the alignment overview panel is opened + by default for a new alignment window. +

+ Show Annotations - If this is selected the new window will + display an annotation panel below the sequences. This annotation + panel may have several rows describing the whole alignment. The 4 + standard annotations Conservation, Quality, + Occupancy and Consensus for the alignment may + be shown or hidden by default using the checkboxes adjacent and + below. +

+ Show group: Conservation and Consensus controls the display + of per-group automatic annotation. +

+ Consensus: Histogram and Logo checkboxes control the + display of the consensus histogram and sequence logo for consensus + annotation rows. +

+ Full Sequence ID - If selected the ID panel will display + the name of a sequence plus the start and end residues in the format + name/start-end. If not selected, the displayed ID will be the name + of the sequence. +

+ Right Align IDs - select to align all sequence IDs to the + left-hand edge of the sequence alignment, rather than the left-hand + edge of the alignment display window. +

+ Font - The default font name, size and style can be set for + a new alignment window. +

+ Sequence ID Tooltip: Control the display of Database + References and Non-positional annotation in the tooltip displayed + when the mouse is over a sequence's ID. +

+ Show Unconserved - When this is selected, all consensus + sequence symbols will be rendered as a '.', highlighting mutations + in highly conserved alignments. +

+ Sequence Name Italics - select to apply the italicised + version of the font to sequence labels. +

+ Smooth Font - Toggles anti-aliasing on / off for faster + rendering of the alignment. +

+ Gap Symbol - The default gap symbol may be set to either + "-" or "." +

+ Wrap Alignment - Select whether to open new alignment + windows in wrapped mode or not. +

+ Sort alignment by - When the alignment is loaded in, it can + be ordered as read (No sort), or sorted by Id or pairwise identity. +

+ Sort annotations by - Annotations can be unsorted, sorted + by the order of the related sequences in the alignment, or by label. + Autocalculated annotations (e.g. Consensus) can be shown either last + (below sequence annotations) or first (above sequence annotations). + Since Jalview 2.8.2. +

+ Open file - If this is selected then the default alignment + file will be opened when Jalview is started. You can change the + default file by clicking on file name and either typing in the file + path or selecting it from the file chooser window.
Note: + The default example alignment is updated periodically to + demonstrate new features in Jalview. +

+ "Colours" + Preferences tab +

+ Alignment Colour - The default colour scheme for a new + alignment window. If the chosen option is "User Defined" + then the last User Defined Colour loaded or saved via the User + Defined Colours panel will be loaded. +

+ Annotation Shading Default - set the default minimum and + maximum colours used when Colour + by Annotation... is selected from the alignment window's colours + menu. +

+ "Overview" + Preferences tab +

+ Use legacy gap colouring (gaps are white) - when enabled, + Jalview's overview shows gaps as white, and sequences with no + colourscheme applied as grey. +

+ Show Hidden regions when opening overview - default setting + for inclusion of hidden regions. +

+ Gap Colour - When legacy gap colouring is not enabled, this + configures the default colour for gaps in the overview. +

+ Hidden Colour - colour used to highlight regions in the + overview that are hidden in the alignment. +

+ Gap Colour - The default colour scheme for a new alignment + window. If the chosen option is "User Defined" then the + last User Defined Colour loaded or saved via the User Defined + Colours panel will be loaded. +

+ "Structure" + Preferences tab added in Jalview 2.8.2 +

+ Process secondary structure from PDB - if selected, then + structure information read from PDB will be processed and annotation + added to associated sequences. +

+ Use RNAView for secondary structure - if selected, the + pyRNA RNAView service (https://github.com/fjossinet/PyRNA) + will be called to derive secondary structure information for RNA + chains. +

+ Add secondary structure annotation to alignment - if + selected, Jmol's + implementation DSSP will be used to add annotation to polypeptide + chains in the structure. +

+ Add Temperature Factor annotation to alignment - if + selected, values extracted from the Temperature Factor column for + the backbone atoms in the PDB file will be extracted as annotation + lines shown on the alignment. +

+ Default structure viewer - choose Jmol or CHIMERA for + viewing 3D structures. +

+ Path to Chimera program - Optional, as Jalview will search + standard installation paths for Windows, Linux or MacOS. If you have + installed Chimera in a non-standard location, you can specify it + here, by entering the full path to the Chimera executable program. + Double-click this field to open a file chooser dialog. +

+ "Connections" + Preferences tab +

+ Default Browser (Unix)
It's difficult in Java to + detect the default web browser for Unix users. If Jalview can't find + your default web browser, enter the name or full path to your web + browser application. +

+ Proxy Server
If you normally use a proxy server + for using the internet, you must tick the box "Use a Proxy + Server" and enter the address and port details as necessary. + Web Services will not work if you are using a proxy server and do + not enter the settings here. +

+ Usage statistics, Questionnaire and Version checks
+ Uncheck these options to prevent Jalview from submitting usage + statistics to google analytics, checking for Jalview questionnaires + or retrieving details of the latest release version (at + www.jalview.org). See the user privacy + statement for more information. +

+ The "Links" Preferences + tab +

+ This panel shows a table, and two sections - Edit and Filter. + The table shows the available URL link definitions (consisting of a + database, Name, and URL template string), a checkbox In + Menu which indicates if the link is enabled, and Double + Click which marks the link that will be opened if a sequence's ID + is double clicked. The table can be sorted by clicking on the column headers. +

Edit Links
This section contains three buttons, + New, Edit and Delete, which allow you to + create, modify and remove user-defined URL links from the Sequence + ID's links submenu. +

+ Filter
The Filter text box allows you to + quickly show rows in the table containing a particular text string. + The Custom only button limits the entries in the table to + just those you have configured yourself via the Edit + Links buttons. Press Show all to clear any filters. +

The links table is prepopulated with persistent URLs for many common + bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not + user editable. + Read more about configuring + URL links. +

+ Output Preferences tab +

+ EPS Rendering Style
This is a selection box which + allows the user to set a default rendering style for EPS export: +

"Prompt each time"
Choose this to be + asked to select between Lineart and Text each time you make an EPS + file. +
"Lineart"
EPS files will accurately + reproduce the alignment view in Jalview and all characters will be + converted into line art. Files generated in this way are large and + are not easily editable, but have no font table dependencies. +
"Text"
EPS files will be a mixture of + text and lineart. This produces compact files that can be edited + easily in programs like Microsoft Word and Adobe Illustrator, but + can be problematic if the fonts available to Jalview are not + accessible by the program reading the EPS file. +

+ Automatically set ID width
When enabled, the + column containing sequence and annotation labels at the left hand + side of an exported figure will be made large enough to display each + sequence ID and annotation label in its own line. Enable this if you + have particularly long sequence IDs and need to generate EPS or PNG + figures or web pages. +

+ Figure ID column width
Manually specify the width + of the left hand column where sequence IDs and annotation labels + will be rendered in exported alignment figures. This setting will be + ignored if "Automatically set ID width" is set. +

+ Sequence/Start-End Numbering
The output tab also + has a group of checkboxes for each file format. If these are ticked, + then Jalview will write files with the start and end sequence + positions appended to each sequence id: +

+   >ID/1-10
+   AACDEAAFEA
+

If the boxes are left unchecked for a particular format, the + sequence limits will not be appended to the sequence id.

+ Embed BioJSON to HTML export +

+ When this option is enabled, Jalview embeds BioJSON data within HTML files + exported from Jalview at generation time. This enables the exported + HTML files to be extracted and imported back into the Jalview + desktop application at a later time. +

+ Use Modeller Output +

+ This option only applies to PIR format output. Jalview automatically + reads PIR files with sequence descriptions compatible with the + program Modeller. If this + option is selected Jalview will + write Modeller style PIR files with correct start/end numbering + and PDB file association (if available). The Jalview id/start-end + option is ignored if Modeller output is selected. +

+ "Editing" Preferences tab +

There are currently three options available which can be + selected / deselected.

+ AutoCalculate Consensus - For large alignments it can be + useful to deselect "Autocalculate Consensus" when editing. + This prevents lengthy calculations which are performed after each + sequence edit. New alignment windows will have their + "Autocalculate Consensus" option set according to this + setting. +

+ Pad Gaps when Editing - New alignment windows will + "Pad Gaps" according to this setting. +

+ Sort with New Tree - When selected, any trees calculated or + loaded onto the alignment will automatically sort the alignment. +

++ "HMMER" Preferences tab ++

If you have installed HMMER tools (available from hmmer.org), ++ then you should specify on this screen the location of the installation (the path to the folder ++ containing binary executable programs). Double-click in the input field to open a file browser.

When this path is configured, the HMMER menu will be ++ enabled in the Alignment window.

+ + diff --cc help/help/html/menus/alwhmmer.html index ce23c4b,0000000..ce23c4b mode 100644,000000..100644 --- a/help/help/html/menus/alwhmmer.html +++ b/help/help/html/menus/alwhmmer.html diff --cc resources/lang/Messages.properties index c25cda8,f095290..33d9359 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@@ -196,16 -192,15 +193,17 @@@ label.colourScheme_%identity = Percenta 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_helixpropensity = Helix Propensity + label.colourScheme_strandpropensity = Strand Propensity + label.colourScheme_turnpropensity = Turn Propensity + label.colourScheme_buriedindex = 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.colourScheme_hmmer-uniprot = HMMER profile v global background +label.colourScheme_hmmer-alignment = HMMER profile v alignment background + label.colourScheme_t-coffeescores = T-Coffee Scores + label.colourScheme_rnahelices = By RNA Helices + label.colourScheme_sequenceid = Sequence ID Colour label.blc = BLC label.fasta = Fasta label.msf = MSF @@@ -1367,58 -1339,69 +1344,127 @@@ label.most_bound_molecules = Most Boun label.most_polymer_residues = Most Polymer Residues label.cached_structures = Cached Structures label.free_text_search = Free Text Search +label.hmmalign = hmmalign +label.use_hmm = HMM profile to use +label.hmmbuild = hmmbuild +label.hmmsearch = hmmsearch +label.installation = Installation +label.hmmer_location = HMMER Binaries Installation Location +label.cygwin_location = Cygwin Binaries Installation Location (Windows) +label.information_annotation = Information Annotation +label.ignore_below_background_frequency = Ignore Below Background Frequency +label.information_description = Information content, measured in bits +warn.no_hmm = No Hidden Markov model found.\nRun hmmbuild or load an HMM file first. +label.no_sequences_found = No matching sequences, or an error occurred. +label.hmmer = HMMER +label.trim_termini = Trim Non-Matching Termini +label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed. +label.no_of_sequences = Number of sequences returned +label.reporting_cutoff = Reporting Cut-off +label.freq_alignment = Use alignment background frequencies +label.freq_uniprot = Use Uniprot background frequencies +label.hmmalign_options = hmmalign options +label.hmmsearch_options = hmmsearch options +label.executable_not_found = The ''{0}'' executable file was not found +warn.command_failed = {0} failed +label.invalid_folder = Invalid Folder +label.number_of_results = Number of Results to Return +label.auto_align_seqs = Automatically Align Fetched Sequences +label.use_accessions = Return Accessions +label.seq_evalue = Sequence E-value Cut-off +label.seq_score = Sequence Score Threshold +label.dom_evalue = Domain E-value Cut-off +label.dom_score = Domain Score Threshold +label.number_of_results_desc = The maximum number of hmmsearch results to display +label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed +label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name +label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E) +label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T) +label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE) +label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT) +label.add_database = Add Database +label.this_alignment = This alignment +warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam. +label.database_for_hmmsearch = The database hmmsearch will search through +label.use_reference = Use Reference Annotation +label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation +label.hmm_name = Alignment HMM Name +label.hmm_name_desc = The name given to the HMM for the alignment +warn.no_reference_annotation = No reference annotation found +label.hmmbuild_for = Build HMM for +label.hmmbuild_for_desc = Build an HMM for the selected sets of sequences +label.alignment = Alignment +label.groups_and_alignment = All groups and alignment +label.groups = All groups +label.selected_group = Selected group +label.use_info_for_height = Use Information Content as Letter Height - action.search = Search ++action.search = Search ++||||||| merged common ancestors ++======= + label.backupfiles_confirm_delete = Confirm delete + label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options) + label.backupfiles_confirm_save_file = Confirm save file + label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file. + label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay. + label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay. + label.backups = Backups + label.backup = Backup + label.backup_files = Backup Files + label.enable_backupfiles = Enable backup files + label.backup_filename_strategy = Backup filename strategy + label.append_to_filename = Append to filename (%n is replaced by the backup number) + label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above. + label.index_digits = Number of digits to use for the backup number (%n) + label.summary_of_backups_scheme = Summary of backup scheme + label.scheme_examples = Scheme examples + label.increment_index = Increase appended text numbers - newest file has largest number. + label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1. + label.keep_files = Deleting old backup files + label.keep_all_backup_files = Do not delete old backup files + label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files + label.autodelete_old_backup_files = Auto-delete old backup files: + label.always_ask = Always ask + label.auto_delete = Automatically delete + label.filename = filename + label.braced_oldest = (oldest) + label.braced_newest = (most recent) + label.configuration = Configuration + label.configure_feature_tooltip = Click to configure variable colour or filters + label.schemes = Schemes + label.customise = Customise + label.custom = Custom + label.default = Default + label.single_file = Single backup + label.keep_all_versions = Keep all versions + label.rolled_backups = Rolled backup files + label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme + label.custom_description = Your own saved scheme + label.default_description = Keep the last three versions of the file + label.single_file_description = Keep the last version of the file + label.keep_all_versions_description = Keep all previous versions of the file + label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest) + label.cancel_changes_description = Cancel changes made to your last saved Custom scheme + label.previously_saved_scheme = Previously saved scheme + label.no_backup_files = NO BACKUP FILES + label.include_backup_files = Include backup files + label.cancel_changes = Cancel changes + label.warning_confirm_change_reverse = Warning!\nIf you change the increment/decrement of the backup filename number, without changing the suffix or number of digits,\nthis may cause loss of backup files created with the previous backup filename scheme.\nAre you sure you wish to do this? + label.change_increment_decrement = Change increment/decrement? + label.was_previous = was {0} + label.newerdelete_replacement_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and replaced by apparently older file\n''{1}''\t(modified {3}, size {5}). + label.confirm_deletion_or_rename = Confirm deletion of ''{0}'' or rename to ''{1}''? + label.newerdelete_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but is newer than the oldest remaining backup file\n''{1}''\t(modified {3}, size {5}). + label.confirm_deletion = Confirm deletion of ''{0}''? + label.delete = Delete + label.rename = Rename + label.keep = Keep + label.file_info = (modified {0}, size {1}) + label.annotation_name = Annotation Name + label.annotation_description = Annotation Description + label.edit_annotation_name_description = Edit Annotation Name/Description + label.alignment = alignment + label.pca = PCA + label.create_image_of = Create {0} image of {1} + label.click_to_edit = Click to edit, right-click for menu + label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu ++>>>>>>> develop diff --cc resources/lang/Messages_es.properties index eb217bd,ec7eb5d..804b115 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@@ -1362,4 -1340,69 +1339,70 @@@ label.most_bound_molecules = Más Molécu label.most_polymer_residues = Más Residuos de Polímeros label.cached_structures = Estructuras en Caché label.free_text_search = Búsqueda de texto libre - action.search = Buscar ++action.search = Buscar + label.backupfiles_confirm_delete = Confirmar borrar + label.backupfiles_confirm_delete_old_files = ¿Borrar los siguientes archivos? (ver la pestaña 'Copias' de la ventana de Preferencias para más opciones) + label.backupfiles_confirm_save_file = Confirmar guardar archivo + label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos. + label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien. + label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien. + label.backups = Respaldos + label.backup = Respaldo + label.backup_files = Archivos de respaldos + label.enable_backupfiles = Habilitar archivos de respaldos + label.backup_filename_strategy = Estrategia de nombres de archivo de respaldos + label.append_to_filename = Adjuntar texto (%n es reemplazado por el número de respaldo) + label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba. + label.index_digits = Número de dígitos a utilizar para el número de respaldo. + label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad + label.scheme_examples = Ejemplos de esquema + label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande + label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1 + label.keep_files = Borrando los respaldos antiguos + label.keep_all_backup_files = No borrar respaldos antiguas + label.keep_only_this_number_of_backup_files = Mantenga solo este número de respaldos más recientes + label.autodelete_old_backup_files = Borrer automáticamente respaldos antiguos: + label.always_ask = Pregunta siempre + label.auto_delete = Borrer automáticamente + label.filename = nombre_de_archivo + label.braced_oldest = (mas antiguo) + label.braced_newest = (mas nuevo) + label.configuration = Configuración + label.configure_feature_tooltip = Haga clic para configurar el color o los filtros + label.schemes = Esquemas + label.customise = Personalizar + label.custom = Personal + label.default = Defecto + label.single_file = Solo uno respaldo + label.keep_all_versions = Mantener todas las versiones + label.rolled_backups = Ciclos respaldos + label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado + label.custom_description = Tu propio esquema guardado + label.default_description = Conserve las últimas tres versiones del archivo + label.single_file_description = Conserve la última versión del archivo + label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo + label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua) + label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado + label.previously_saved_scheme = Esquema previamente guardado + label.no_backup_files = NO ARCHIVOS DE RESPALDOS + label.include_backup_files = Incluir archivos de respaldos + label.cancel_changes = Cancelar cambios + label.warning_confirm_change_reverse = ¡Advertencia!\nSi cambia el incremento/decremento del número de archivos de respaldos, sin cambiar el sufijo o número de dígitos,\nesto puede causar la pérdida de los archivos de respaldos creados con el esquema anterior de nombre de archivo de respaldos.\n¿Está seguro de que desea hacer esto? + label.change_increment_decrement = ¿Cambiar de incremento/decremento? + label.was_previous = era {0} + label.newerdelete_replacement_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado y reemplazarse por un archivo aparentemente más antiguo\n''{1}''\t(modificado {3}, tamaño {5}). + label.confirm_deletion_or_rename = Confirmar borrar ''{0}'', o cambiar el nombre a ''{1}''? + label.newerdelete_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado pero es mas nuevo que el archivo de respaldo restante más antiguo\n''{1}''\t(modified {3}, size {5}). + label.confirm_deletion = Confirmar eliminar ''{0}''? + label.delete = Borrar + label.rename = Cambiar + label.keep = Mantener + label.file_info = (modificado {0}, tamaño {1}) + label.annotation_name = Nombre de la anotación + label.annotation_description = Descripción de la anotación + label.edit_annotation_name_description = Editar el nombre/descripción de la anotación + label.alignment = alineamiento + label.pca = ACP + label.create_image_of = Crear imagen {0} de {1} + label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú + label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores diff --cc src/jalview/api/AlignViewportI.java index 6b3cbe8,389d9cf..ab0aeed --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@@ -495,21 -487,35 +495,49 @@@ public interface AlignViewportI extend @Override void setProteinFontAsCdna(boolean b); - public abstract TreeModel getCurrentTree(); + void setHmmProfiles(ProfilesI info); + + ProfilesI getHmmProfiles(); + + /** + * Registers and starts a worker thread to calculate Information Content + * annotation, if it is not already registered + * + * @param ap + */ + void initInformationWorker(AlignmentViewPanel ap); + + boolean isInfoLetterHeight(); + + abstract TreeModel getCurrentTree(); - public abstract void setCurrentTree(TreeModel tree); + abstract void setCurrentTree(TreeModel tree); + + /** + * @param update + * - set the flag for updating structures on next repaint + */ + void setUpdateStructures(boolean update); + + /** + * + * @return true if structure views will be updated on next refresh + */ + boolean isUpdateStructures(); + + /** + * check if structure views need to be updated, and clear the flag afterwards. + * + * @return if an update is needed + */ + boolean needToUpdateStructureViews(); + + /** + * Adds sequencegroup to the alignment in the view. Also adds a group to the + * complement view if one is defined. + * + * @param sequenceGroup + * - a group defined on sequences in the alignment held by the view + */ + void addSequenceGroup(SequenceGroup sequenceGroup); } diff --cc src/jalview/datamodel/AlignmentI.java index d591f42,93a2456..7386d4b --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@@ -579,23 -595,15 +593,25 @@@ public interface AlignmentI extends Ann AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo); /** - * Set the hidden columns collection on the alignment + * Set the hidden columns collection on the alignment. Answers true if the + * hidden column selection changed, else false. * * @param cols + * @return */ - public void setHiddenColumns(HiddenColumns cols); + public boolean setHiddenColumns(HiddenColumns cols); /** + * Insert a sequence at a position in an alignment + * + * @param i + * The index of the position. + * @param snew + * The new sequence. + */ + void insertSequenceAt(int i, SequenceI snew); + + /** * Set the first sequence as representative and hide its insertions. Typically * used when loading JPred files. */ diff --cc src/jalview/datamodel/SequenceGroup.java index cffe0d9,3bf7bc4..56681cf --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@@ -45,53 -43,62 +45,53 @@@ import java.util.Map public class SequenceGroup implements AnnotatedCollectionI { // TODO ideally this event notification functionality should be separated into - // a - // subclass of ViewportProperties similarly to ViewportRanges. Done here as - // quick fix for JAL-2665 + // a subclass of ViewportProperties similarly to ViewportRanges. + // Done here as a quick fix for JAL-2665 public static final String SEQ_GROUP_CHANGED = "Sequence group changed"; - protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( - this); + private String groupName; - public void addPropertyChangeListener(PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } + private String description; - public void removePropertyChangeListener(PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } - // end of event notification functionality initialisation + private AnnotatedCollectionI context; - String groupName; + private Conservation conservationData; - String description; + private ProfilesI consensusProfiles; - Conservation conserve; + private ProfilesI hmmProfiles; - boolean displayBoxes = true; + private boolean displayBoxes = true; - boolean displayText = true; + private boolean displayText = true; - boolean colourText = false; + private boolean colourText = false; - /** - * True if the group is defined as a group on the alignment, false if it is - * just a selection. + /* + * true if the group is defined as a group on the alignment, false if it is + * just a selection */ - boolean isDefined = false; + private boolean isDefined; - /** + /* * after Olivier's non-conserved only character display */ - boolean showNonconserved = false; + private boolean showNonconserved; - /** - * group members + /* + * sequences in the group */ - private List sequences = new ArrayList<>(); + private List sequences; - /** + /* * representative sequence for this group (if any) */ - private SequenceI seqrep = null; + private SequenceI seqrep; - int width = -1; + private int width = -1; - /** - * Colourscheme applied to group if any + /* + * colour scheme applied to group if any */ public ResidueShaderI cs; @@@ -262,19 -244,17 +268,30 @@@ } } + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + + /** + * Constructor that copies the given list of sequences + * + * @param seqs + */ + public SequenceGroup(List seqs) + { + this(); + this.sequences.addAll(seqs); + } + public boolean isShowSequenceLogo() { return showSequenceLogo; diff --cc src/jalview/gui/AlignFrame.java index 5fa168d,f3a8ab5..4587368 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -62,14 -63,9 +63,15 @@@ import jalview.datamodel.SequenceGroup import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMAlign; +import jalview.hmmer.HMMBuild; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearch; +import jalview.hmmer.HmmerCommand; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; + import jalview.io.BackupFiles; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@@ -139,14 -131,14 +141,15 @@@ import java.net.URL import java.util.ArrayList; import java.util.Arrays; import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; +import java.util.HashSet; import java.util.List; +import java.util.Set; import java.util.Vector; + import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; +import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; diff --cc src/jalview/gui/AlignViewport.java index 39ded7f,bc668fd..847084d --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@@ -318,10 -302,13 +318,11 @@@ public class AlignViewport extends Alig if (residueShading != null) { - residueShading.setConsensus(hconsensus); + residueShading.setConsensus(consensusProfiles); } + setColourAppliesToAllGroups(true); } - boolean validCharWidth; - /** * {@inheritDoc} */ diff --cc src/jalview/gui/AnnotationLabels.java index dc89fa3,6da6cc3..8aac7dc --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@@ -420,180 -414,31 +420,189 @@@ public class AnnotationLabels extends J } else if (label.indexOf("Consensus") > -1) { - addConsensusMenu(pop, ann); + addConsensusMenuOptions(ap, aa[selectedRow], pop); + + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); } + else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId())) + { + addHmmerMenu(pop, ann); + } } pop.show(this, evt.getX(), evt.getY()); } /** + * Adds context menu options for (alignment or group) Hmmer annotation + * + * @param pop + * @param ann + */ + protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann) + { + final boolean isGroupAnnotation = ann.groupRef != null; + pop.addSeparator(); + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString( + "label.ignore_below_background_frequency"), + isGroupAnnotation + ? ann.groupRef + .isIgnoreBelowBackground() + : ap.av.isIgnoreBelowBackground()); + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (isGroupAnnotation) + { + if (!ann.groupRef.isUseInfoLetterHeight()) + { + ann.groupRef.setIgnoreBelowBackground(cbmi.getState()); + // todo and recompute group annotation + } + } + else if (!ap.av.isInfoLetterHeight()) + { + ap.av.setIgnoreBelowBackground(cbmi.getState(), ap); + // todo and recompute annotation + } + ap.alignmentChanged(); // todo not like this + } + }); + pop.add(cbmi); + final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem( + MessageManager.getString("label.use_info_for_height"), + isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight() + : ap.av.isInfoLetterHeight()); + letterHeight.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (isGroupAnnotation) + { + ann.groupRef.setInfoLetterHeight((letterHeight.getState())); + ann.groupRef.setIgnoreBelowBackground(true); + // todo and recompute group annotation + } + else + { + ap.av.setInfoLetterHeight(letterHeight.getState(), ap); + ap.av.setIgnoreBelowBackground(true, ap); + // todo and recompute annotation + } + ap.alignmentChanged(); + } + }); + pop.add(letterHeight); + if (isGroupAnnotation) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + ann.groupRef.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef.setShowInformationHistogram(chist.getState()); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + ann.groupRef.isShowHMMSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef.setShowHMMSequenceLogo(cprofl.getState()); + ap.repaint(); + } + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + ann.groupRef.isNormaliseHMMSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef + .setNormaliseHMMSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + ann.groupRef.setShowHMMSequenceLogo(true); + ap.repaint(); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowInformationHistogram(chist.getState()); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowHMMSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowHMMSequenceLogo(cprof.getState()); + ap.repaint(); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseHMMSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowHMMSequenceLogo(true); + av.setNormaliseHMMSequenceLogo(cprofnorm.getState()); + ap.repaint(); + } + }); + pop.add(cprofnorm); + } + } + + /** - * Adds context menu options for (alignment or group) Consensus annotation + * A helper method that adds menu options for calculation and visualisation of + * group and/or alignment consensus annotation to a popup menu. This is + * designed to be reusable for either unwrapped mode (popup menu is shown on + * component AnnotationLabels), or wrapped mode (popup menu is shown on + * IdPanel when the mouse is over an annotation label). * - * @param pop + * @param ap * @param ann + * @param pop */ - protected void addConsensusMenu(JPopupMenu pop, - final AlignmentAnnotation ann) + static void addConsensusMenuOptions(AlignmentPanel ap, + AlignmentAnnotation ann, + JPopupMenu pop) { - final boolean isGroupAnnotation = ann.groupRef != null; pop.addSeparator(); final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( diff --cc src/jalview/gui/CalculationChooser.java index eaaf0a5,336a312..9abef1f --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@@ -23,12 -23,11 +23,13 @@@ package jalview.gui import jalview.analysis.TreeBuilder; import jalview.analysis.scoremodels.ScoreModels; import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.AlignViewportI; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; + import jalview.bin.Cache; import jalview.datamodel.SequenceGroup; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.Color; diff --cc src/jalview/gui/Preferences.java index 3259909,9754e0d..a0a7511 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@@ -24,7 -24,8 +24,9 @@@ import jalview.analysis.AnnotationSorte import jalview.bin.Cache; import jalview.gui.Help.HelpId; import jalview.gui.StructureViewer.ViewerType; +import jalview.hmmer.HmmerCommand; + import jalview.io.BackupFiles; + import jalview.io.BackupFilesPresetEntry; import jalview.io.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; diff --cc src/jalview/gui/WsParamSetManager.java index ab03d69,cb98856..43da8dd --- a/src/jalview/gui/WsParamSetManager.java +++ b/src/jalview/gui/WsParamSetManager.java @@@ -214,9 -226,9 +228,10 @@@ public class WsParamSetManager implemen } paramFiles = paramFiles.concat(filename); } - jalview.bin.Cache.setProperty(WS_PARAM_FILES, paramFiles); - Cache.setProperty("WS_PARAM_FILES", paramFiles); + - jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet(); ++ Cache.setProperty(WS_PARAM_FILES, paramFiles); + + WebServiceParameterSet paramxml = new WebServiceParameterSet(); paramxml.setName(parameterSet.getName()); paramxml.setDescription(parameterSet.getDescription()); diff --cc src/jalview/io/StockholmFile.java index 58b171d,0e73af1..61f28a9 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@@ -87,33 -83,17 +87,43 @@@ public class StockholmFile extends Alig public static final Regex DETECT_BRACKETS = new Regex( "(<|>|\\[|\\]|\$|\$|\\{|\\})"); + /* + * lookup table of Stockholm 'feature' (annotation) types + * see http://sonnhammer.sbc.su.se/Stockholm.html + */ + private static Map featureTypes = null; + + // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first. + public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"; + + // use the following regex to decide an annotations (whole) line is NOT an RNA + // SS (it contains only E,H,e,h and other non-brace/non-alpha chars) + private static final Regex NOT_RNASS = new Regex( + "^[^<>[\\](){}A-DF-Za-df-z]*$"); + + StringBuffer out; // output buffer + - AlignmentI al; + static + { + featureTypes = new HashMap<>(); + featureTypes.put("SS", "Secondary Structure"); + featureTypes.put("SA", "Surface Accessibility"); + featureTypes.put("TM", "transmembrane"); + featureTypes.put("PP", "Posterior Probability"); + featureTypes.put("LI", "ligand binding"); + featureTypes.put("AS", "active site"); + featureTypes.put("IN", "intron"); + featureTypes.put("IR", "interacting residue"); + featureTypes.put("AC", "accession"); + featureTypes.put("OS", "organism"); + featureTypes.put("CL", "class"); + featureTypes.put("DE", "description"); + featureTypes.put("DR", "reference"); + featureTypes.put("LO", "look"); + featureTypes.put("RF", "Reference Positions"); + } + + private AlignmentI al; public StockholmFile() { @@@ -891,7 -831,9 +901,10 @@@ : label; } boolean ss = false, posterior = false; - type = typeToDescription(type); + type = id2type(type); + + boolean isrnass = false; ++ if (type.equalsIgnoreCase("secondary structure")) { ss = true; @@@ -1184,13 -1126,23 +1200,22 @@@ String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character.toString(sequenceI.getCharAt(k))) - : annot.displayCharacter; + : (annot.displayCharacter == null + ? String.valueOf(annot.secondaryStructure) + : annot.displayCharacter); + if (ch == null) + { + ch = " "; + } if (key != null && key.equals("SS")) { + char ssannotchar = ' '; + boolean charset = false; if (annot == null) { - // sensible gap character - ssannotchar = ' '; - charset = true; ++ // TODO: TVA: Check against develop for correct behaviour! + // Stockholm format requires underscore, not space + return UNDERSCORE; } else { @@@ -1214,9 -1171,82 +1244,11 @@@ { seq = ch.charAt(1); } - return seq; + + return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.' + : seq; } - public String print() - { - out = new StringBuffer(); - out.append("# STOCKHOLM 1.0"); - out.append(newline); - print(getSeqsAsArray(), false); - - out.append("//"); - out.append(newline); - return out.toString(); - } - - private static Hashtable typeIds = null; - - static - { - if (typeIds == null) - { - typeIds = new Hashtable(); - typeIds.put("SS", "Secondary Structure"); - typeIds.put("SA", "Surface Accessibility"); - typeIds.put("TM", "transmembrane"); - typeIds.put("PP", "Posterior Probability"); - typeIds.put("LI", "ligand binding"); - typeIds.put("AS", "active site"); - typeIds.put("IN", "intron"); - typeIds.put("IR", "interacting residue"); - typeIds.put("AC", "accession"); - typeIds.put("OS", "organism"); - typeIds.put("CL", "class"); - typeIds.put("DE", "description"); - typeIds.put("DR", "reference"); - typeIds.put("LO", "look"); - typeIds.put("RF", "Reference Positions"); - - } - } - - protected static String id2type(String id) - { - if (typeIds.containsKey(id)) - { - return (String) typeIds.get(id); - } - System.err.println( - "Warning : Unknown Stockholm annotation type code " + id); - return id; - } - - protected static String type2id(String type) - { - String key = null; - Enumeration e = typeIds.keys(); - while (e.hasMoreElements()) - { - Object ll = e.nextElement(); - if (typeIds.get(ll).toString().equalsIgnoreCase(type)) - { - key = (String) ll; - break; - } - } - if (key != null) - { - return key; - } - System.err.println( - "Warning : Unknown Stockholm annotation type: " + type); - return key; - } - /** * make a friendly ID string. * diff --cc src/jalview/jbgui/GAlignFrame.java index e71d548,075b490..c228c90 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@@ -25,9 -27,8 +27,10 @@@ import jalview.api.SplitContainerI import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; +import jalview.hmmer.HmmerCommand; +import jalview.io.FileFormatException; import jalview.io.FileFormats; + import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; import jalview.util.Platform; @@@ -271,17 -262,17 +273,17 @@@ public class GAlignFrame extends JInter saveAs_actionPerformed(e); } }; - + // FIXME getDefaultToolkit throws an exception in Headless mode KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, false); addMenuActionAndAccelerator(keyStroke, saveAs, al); - + closeMenuItem.setText(MessageManager.getString("action.close")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@@ -975,10 -959,10 +977,10 @@@ } }; addMenuActionAndAccelerator(keyStroke, unGroup, al); - + copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @@@ -989,10 -973,10 +991,10 @@@ } }; addMenuActionAndAccelerator(keyStroke, copy, al); - + cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@@ -1610,10 -1591,10 +1629,10 @@@ tabbedPane_focusGained(e); } }); - + JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override diff --cc src/jalview/jbgui/GPreferences.java index a3921f6,60bf1b7..c1afbf7 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@@ -23,10 -24,16 +24,17 @@@ import jalview.bin.Cache import jalview.fts.core.FTSDataColumnPreferences; import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; import jalview.fts.service.pdb.PDBFTSRestClient; + import jalview.gui.Desktop; + import jalview.gui.JalviewBooleanRadioButtons; + import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer.ViewerType; + import jalview.io.BackupFilenameParts; + import jalview.io.BackupFiles; + import jalview.io.BackupFilesPresetEntry; + import jalview.io.IntKeyStringValueEntry; import jalview.util.MessageManager; +import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; @@@ -41,14 -48,16 +49,17 @@@ import java.awt.Insets import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; + import java.awt.event.KeyListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; + import java.util.Arrays; + import java.util.List; +import javax.swing.AbstractButton; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; +import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.DefaultListCellRenderer; import javax.swing.JButton; @@@ -275,33 -283,55 +293,72 @@@ public class GPreferences extends JPane protected JCheckBox sortByTree = new JCheckBox(); /* + * hmmer tab and components + */ + protected JPanel hmmerTab; + + protected JCheckBox hmmrTrimTermini; + + protected AbstractButton hmmerBackgroundUniprot; + + protected AbstractButton hmmerBackgroundAlignment; + + protected JTextField hmmerSequenceCount; + + protected JTextField hmmerPath; + + protected JTextField cygwinPath; + + /* - * DAS Settings tab + * Web Services tab */ - protected JPanel dasTab = new JPanel(); + protected JPanel wsTab = new JPanel(); /* - * Web Services tab + * Backups tab components + * a lot of these are member variables instead of local variables only so that they + * can be enabled/disabled easily in one go */ - protected JPanel wsTab = new JPanel(); + protected JCheckBox enableBackupFiles = new JCheckBox(); + + protected JPanel presetsPanel = new JPanel(); + + protected JLabel presetsComboLabel = new JLabel(); + + protected JCheckBox customiseCheckbox = new JCheckBox(); + + protected JButton revertButton = new JButton(); + + protected JComboBox