JNet Secondary Structure Prediction

From: gmungoc Date: Tue, 17 Jan 2017 16:08:58 +0000 (+0000) Subject: Merge branch 'features/JAL-2295setChimeraAttributes' into spikes/mungo X-Git-Tag: Release_2_11_0~62^2~32 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8677e6e34e291edc58c1da2fc9c958473754143f;hp=fd9e6f7e0424bb69e46443d7d96237d99e792c03;p=jalview.git Merge branch 'features/JAL-2295setChimeraAttributes' into spikes/mungo --- diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html index 7b4daee..e9c22e5 100644 --- a/examples/appletDeployment.html +++ b/examples/appletDeployment.html @@ -195,7 +195,7 @@ 2.1

Jalview Applet can read and display JNet secondary structure annotation +
Jalview Applet can read and display JPred secondary structure annotation directly via the jnetfile parameter.
Param "UserDefinedColour" - specify your own colours for each residue using a semi colon diff --git a/examples/appletParameters.html b/examples/appletParameters.html index cc95ecb..277fd69 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -91,8 +91,9 @@ the applet can be interacted with via its jnetfile fileName Secondary structure predictions from a Jnet Concise - file will be added to the first sequence in the alignment. + href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred Concise + file will be added to the first sequence in the alignment.
+ jpredfile can be used interchangeably with this parameter. PDBfile(x) diff --git a/examples/applets.html b/examples/applets.html index d997f14..b789672 100644 --- a/examples/applets.html +++ b/examples/applets.html @@ -136,7 +136,7 @@ Try out JalviewLite by pressing one of the buttons below. Displays a Multiple Sequence Alignment - Based JNet Prediction for a Sequence + Based JPred Prediction for a Sequence
diff --git a/examples/groovy/fileFormat.groovy b/examples/groovy/fileFormat.groovy new file mode 100644 index 0000000..c314a6c --- /dev/null +++ b/examples/groovy/fileFormat.groovy @@ -0,0 +1,108 @@ +import jalview.datamodel.AlignmentI +import jalview.datamodel.SequenceI +import jalview.datamodel.Sequence +import jalview.io.FileFormatI +import jalview.io.FileFormats +import jalview.io.FileParse +import jalview.io.AlignFile + +/* + * Example script that registers a new alignment file format + * consisting of lines like + * !I= + * !S= + */ + +/* + * A parser class to read or write the format + */ +class MyParser extends AlignFile +{ + /* + * Constructor for reading a file; the superclass + * constructor will call the parse() method + */ + MyParser(FileParse src) + { + super(src) + } + + /* + * Constructor for writing out an alignment + */ + MyParser(AlignmentI al) + { + } + + /* + * Parse a formatted data file (with no error checking!) + */ + void parse() + { + String id + String line + while ((line = nextLine()) != null) + { + if (line.startsWith('!I=')) + { + int pos = line.indexOf('/') + id = line.substring(3, pos == -1 ? line.length() : pos) + } else if (line.startsWith('!S=')) + { + String seq = line.substring(3) + addSequence(new Sequence(id, seq)) + } + } + } + + /* + * Print the formatted sequences + * (addSuffix always defaults to true as no user preference for it) + */ + String print(SequenceI[] seqs, boolean addSuffix) + { + StringBuilder sb = new StringBuilder() + for (SequenceI seq : seqs) + { + sb.append('!I=').append(seq.getDisplayId(addSuffix)).append('\n') + sb.append('!S=').append(seq.getSequenceAsString()).append('\n') + } + sb.toString() + } +} + +/* + * A closure that defines the 'Groovy example' file format, + * delegating to MyParser for reading and writing + */ +def myFormat = { -> + [ + getName: { -> 'Groovy example' }, + + toString: { -> getName() }, + + getExtensions: { -> 'grv' }, + + getReader: { FileParse source -> new MyParser(source) }, + + getWriter: { AlignmentI al -> new MyParser(al) }, + + isReadable: { -> true }, + + isWritable: { -> true }, + + isTextFormat: { -> true }, + + isStructureFile: { -> false }, + + isComplexAlignFile: { -> false }, + + ] as FileFormatI +} + +/* + * Register the file format. After running this script in Jalview's + * Groovy console, the new format should be shown in open file, + * save file, and output to textbox menu options. + */ +FileFormats.instance.registerFileFormat(myFormat()) diff --git a/help/help.jhm b/help/help.jhm index e034fc2..f69ed00 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -33,7 +33,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 3a6b0b3..54abd53 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -70,7 +70,7 @@ - + diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html index a79541b..7c0e3dc 100644 --- a/help/html/calculations/referenceseq.html +++ b/help/html/calculations/referenceseq.html @@ -58,7 +58,7 @@
Defining a reference when importing annotation
Jalview automatically assigns a reference sequence when importing analysis results, such as those returned - from JPred4 . A reference + from JPred . A reference sequence can also be assigned via the SET_REF command in an alignment annotation file.

JPred Secondary Structure Prediction
Secondary structure prediction by network - consensus. See the Jpred3 + consensus. See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:

If nothing is selected, and the displayed - sequences appear to be aligned, then a JNet prediction + sequences appear to be aligned, then a JPred prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.

If just one sequence (or a region on one sequence) has been selected, it will be submitted to - the automatic JNet prediction server for homolog + the automatic JPred prediction server for homolog detection and prediction.

If a set of sequences are selected, and they appear to be aligned, then the alignment will be used - for a Jnet prediction on the first + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 33282e9..b71bc1a 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -68,22 +68,22 @@

JPred Secondary Structure Prediction
Secondary structure prediction by network consensus. - See the Jpred3 client + See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:

If nothing is selected, and the displayed - sequences appear to be aligned, then a JNet prediction + sequences appear to be aligned, then a JPred prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.

If just one sequence (or a region on one sequence) has been selected, it will be submitted to the - automatic JNet prediction server for homolog detection + automatic JPred prediction server for homolog detection and prediction.

If a set of sequences are selected, and they appear to be aligned, then the alignment will be used - for a Jnet prediction on the first + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 396a3a7..077ace6 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -20,10 +20,10 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -JNet Secondary Structure Prediction +JPred Secondary Structure Prediction - JNet Secondary Structure Prediction + JPred Secondary Structure Prediction
Secondary structure prediction methods attempts to infer the likely secondary structure for a protein based on its amino acid @@ -52,35 +52,35 @@
The function available from the Web Service→Secondary Structure - Prediction→JNet Secondary Structure Prediction menu does two + Prediction→JPred Secondary Structure Prediction menu does two different kinds of prediction, dependent upon the currently selected region:

If nothing is selected, and the displayed sequences appear - to be aligned, then a JNet prediction will be run for the first + to be aligned, then a JPred prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.

If just one sequence (or a region on one sequence) has been - selected, it will be submitted to the automatic JNet prediction + selected, it will be submitted to the automatic JPred prediction server for homolog detection and prediction.

If a set of sequences are selected, and they appear to be - aligned, then the alignment will be used for a Jnet prediction on + aligned, then the alignment will be used for a JPred prediction on the first sequence selected in the set (that is, the one nearest the top of the alignment window).

- Note: JNet secondary structure prediction is a + Note: JPred secondary structure prediction is a 'non-column-separable' service - predictions are based on the sequence profile of contiguous stretches of amino-acid sequence. A prediction will only be made on the visible parts of a sequence (see hiding columns) as if it were a contiguous polypeptide chain. Prediction accuracy at the hidden column boundaries may therefore be less than indicated by - JNet's own reliability score (see below). + JPred's own reliability score (see below).
-
The result of a JNet prediction for a sequence is a new +
The result of a JPred prediction for a sequence is a new annotated alignment window:

The sequence for which the prediction was made is the first one @@ -124,12 +124,12 @@ significantly different primary predictions.

- JNet annotation created in Jalview 2.8.2 and later versions + JPred annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the Add reference annotation Sequence ID popup menu option. - As of Jalview 2.6, the Jnet service accessed accessed via the + As of Jalview 2.6, the JPred service accessed accessed via the 'Secondary structure prediction' submenu should be considered a legacy Jalview SOAP service, and will be replaced in the near future by a JPred4 Rest service. diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index ce39010..f1e371d 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -837,7 +837,7 @@ label.colour_by = Colour by... label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment -label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction +label.jnet_secondary_structure_prediction = JPred Secondary Structure Prediction label.multiharmony = Multi-Harmony label.unable_start_web_service_analysis = Unable to start web service analysis label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages. @@ -971,7 +971,7 @@ error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero leng error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object! error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0} -error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented +error.multiple_jnet_subjob_merge_not_implemented = Multiple JPred subjob merging not yet implemented label.job_never_ran = Job never ran - input returned to user. error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0} @@ -1079,7 +1079,7 @@ exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception w exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment exception.unknown_format_for_file = Unknown format {0} for file \: \n{1} label.remove_gaps = Remove Gaps -exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence! +exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JPred Query sequence! exception.server_timeout_try_later = Server timed out - try again later\n exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later. exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0} @@ -1101,7 +1101,7 @@ info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it ex info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n info.no_jobs_ran = No jobs ran info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1} -info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2} +info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JPred job result data\!\n{2} info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n info.alignment_object_method_notes = \nAlignment Object Method Notes\n info.server_exception = \n{0} Server exception\!\n{1} diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index e5b5e27..8cdcd52 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -768,7 +768,7 @@ label.colour_by = Colorear por... label.muscle_multiple_protein_sequence_alignment = Alineamiento múltiple de secuencias de proteínas con Muscle label.mafft_multiple_sequence_alignment = Alineamiento múltiple de secuencias con MAFFT label.clustalw_multiple_sequence_alignment = Alineamiento múltiple de secuencias con ClustalW -label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JNet +label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JPred label.multiharmony = Multi-Harmony label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview. @@ -902,7 +902,7 @@ error.cannot_have_zero_length_vector_replacement_strings = No es posible tener u error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = ¡Error de implementación! Todavía no se soportan varios trabajos de predicción asociados a una única secuencia. error.implementation_error_invalid_msa_index_for_job = ¡Error de implementación! Valor msaIndex no válido para JPredJob en el objeto de entrada MSA padre! error.implementation_error_startjob_called = Error de implementación - StartJob(JpredJob) invocado en {0} -error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JNet conjuntos. +error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JPred conjuntos. label.job_never_ran = El trabajo nunca se ejecutó - entrada devuelta al usuario. error.implementation_error_minlen_must_be_greater_zero = Error de implementación: minlen debe ser cero o más error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0} @@ -1010,7 +1010,7 @@ exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada c exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento exception.unknown_format_for_file = Formato desconocido {0} para el fichero \: \n{1} label.remove_gaps = Eliminar huecos -exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JNet Query! +exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JPred Query! exception.server_timeout_try_later = Tiempo de conexi\u00F3n ha expirado - int\u00E9ntelo de nuevo m\u00E1s tarde\n exception.web_service_returned_null_try_later= El servidor {0} ha devuelto un objeto nulo, por lo que probablemente no se haya podido contactar con él. Inténtelo de nuevo más tarde. exception.cannot_contact_service_endpoint_at = No es posible contactar por el punto de acceso al servicio en {0} @@ -1031,7 +1031,7 @@ info.job_couldnt_be_run_exceeded_hard_limit = No es posible ejecutar el trabajo info.job_couldnt_be_run_incorrect_param_setting = No es posible ejecutar el trabjao porque el servidor no soporta algunos de los par\u00E1metros.\n{0}\nPor favor, aseg\u00FArese de que ha usado los par\u00E1metros adecuados para este servicio\n info.no_jobs_ran = No se ha ejecutado ningún trabajo info.failed_to_submit_prediction = Error al enviar la predicci\u00F3n\:\n{0} {1} -info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JNet no v\u00E1lidos\!\n{2} +info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JPred no v\u00E1lidos\!\n{2} info.failed_to_submit_sequences_for_alignment = Error al enviar la secuencias para el alineamiento.\nLo m\u00E1s probable es que haya un problema en el servidor.\nSimplemente, cierre la ventana\n info.alignment_object_method_notes = \nNotas sobre los m\u00E9todos del objeto alineamiento\n info.server_exception = \n{0} Excepci\u00F3n del servidor\!\n{1} diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 015734f..8f7a15b 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -36,7 +36,8 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; -import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.SequenceAnnotationReport; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -216,7 +217,7 @@ public class APopupMenu extends java.awt.PopupMenu implements e.printStackTrace(); } - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { MenuItem item = new MenuItem(ff); @@ -244,8 +245,12 @@ public class APopupMenu extends java.awt.PopupMenu implements { menu1.setLabel(MessageManager.getString("action.edit_group")); groupMenu.remove(createGroupMenuItem); + if (sg.cs != null) + { + abovePIDColour.setState(sg.cs.getThreshold() > 0); + conservationMenuItem.setState(sg.cs.conservationApplied()); + } } - } else { @@ -500,23 +505,28 @@ public class APopupMenu extends java.awt.PopupMenu implements @Override public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == abovePIDColour) + Object source = evt.getSource(); + if (source == abovePIDColour) { abovePIDColour_itemStateChanged(); } - else if (evt.getSource() == showColourText) + else if (source == conservationMenuItem) + { + conservationMenuItem_itemStateChanged(); + } + else if (source == showColourText) { showColourText_itemStateChanged(); } - else if (evt.getSource() == showText) + else if (source == showText) { showText_itemStateChanged(); } - else if (evt.getSource() == showBoxes) + else if (source == showBoxes) { showBoxes_itemStateChanged(); } - else if (evt.getSource() == displayNonconserved) + else if (source == displayNonconserved) { this.showNonconserved_itemStateChanged(); } @@ -579,10 +589,6 @@ public class APopupMenu extends java.awt.PopupMenu implements { noColourmenuItem_actionPerformed(); } - else if (source == conservationMenuItem) - { - conservationMenuItem_itemStateChanged(); - } else if (source == unGroupMenuItem) { unGroupMenuItem_actionPerformed(); @@ -784,7 +790,8 @@ public class APopupMenu extends java.awt.PopupMenu implements // now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here - FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter().formatSequences(fileFormat, ap.av.getShowJVSuffix(), ap, true)); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index f830fe6..86dc19b 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -52,6 +52,8 @@ import jalview.io.AppletFormatAdapter; 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; @@ -1362,7 +1364,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, "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())); @@ -1480,10 +1483,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) @@ -3236,7 +3242,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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); diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index d50fcef..c658734 100644 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.io.AlignmentFileI; +import jalview.io.AlignmentFileReaderI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; @@ -68,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, AlignFrame alignFrame; - AlignmentFileI source = null; + AlignmentFileReaderI source = null; public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame) { diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 8d6e683..4278744 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1425,19 +1425,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup == null) { - stretchGroup = av.getAlignment().findGroup(sequence); - if (stretchGroup != null && res > stretchGroup.getStartRes() - && res < stretchGroup.getEndRes()) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } + stretchGroup = av.getAlignment().findGroup(sequence, res); + av.setSelectionGroup(stretchGroup); } - else if (!stretchGroup.getSequences(null).contains(sequence) + if (stretchGroup == null + || !stretchGroup.getSequences(null).contains(sequence) || stretchGroup.getStartRes() > res || stretchGroup.getEndRes() < res) { diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 9fd8a90..d7b064a 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -38,8 +38,8 @@ import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; -import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; import jalview.io.JPredFile; @@ -517,7 +517,7 @@ public class JalviewLite extends Applet implements { try { - FileFormatI theFormat = FileFormat.valueOf(format); + FileFormatI theFormat = FileFormats.getInstance().forName(format); boolean seqlimits = suffix.equalsIgnoreCase(TRUE); if (alf.viewport.getSelectionGroup() != null) { @@ -715,7 +715,7 @@ public class JalviewLite extends Applet implements { boolean seqlimits = suffix.equalsIgnoreCase(TRUE); - FileFormatI theFormat = FileFormat.valueOf(format); + FileFormatI theFormat = FileFormats.getInstance().forName(format); String reply = new AppletFormatAdapter().formatSequences(theFormat, alf.viewport.getAlignment(), seqlimits); return reply; @@ -2255,6 +2255,11 @@ public class JalviewLite extends Applet implements { boolean result = false; String param = applet.getParameter("jnetfile"); + if (param == null) + { + // jnet became jpred around 2016 + param = applet.getParameter("jpredfile"); + } if (param != null) { try diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java index 156e146..d6fb090 100644 --- a/src/jalview/bin/JalviewLiteURLRetrieve.java +++ b/src/jalview/bin/JalviewLiteURLRetrieve.java @@ -25,6 +25,7 @@ import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; @@ -115,7 +116,8 @@ public class JalviewLiteURLRetrieve extends Applet + " cannot be read with protocol==" + protocol); return; } - FileFormatI format = FileFormat.valueOf(getParameter("format")); + FileFormatI format = FileFormats.getInstance().forName( + getParameter("format")); if (format == null) { format = new IdentifyFile().identify(file, protocol); diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index d651c1d..90bdcae 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -366,17 +366,18 @@ public class Alignment implements AlignmentI * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI) */ @Override - public SequenceGroup findGroup(SequenceI s) + public SequenceGroup findGroup(SequenceI seq, int position) { synchronized (groups) { - for (int i = 0; i < this.groups.size(); i++) + for (SequenceGroup sg : groups) { - SequenceGroup sg = groups.get(i); - - if (sg.getSequences(null).contains(s)) + if (sg.getSequences(null).contains(seq)) { - return sg; + if (position >= sg.getStartRes() && position <= sg.getEndRes()) + { + return sg; + } } } } diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 7274e5f..2df099a 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -156,15 +156,16 @@ public interface AlignmentI extends AnnotatedCollectionI int findIndex(SequenceI s); /** - * Finds group that given sequence is part of. + * Returns the first group (in the order in which groups were added) that + * includes the given sequence and aligned position (base 0), or null if none + * found * - * @param s - * Sequence in alignment. + * @param seq + * @param position * - * @return First group found for sequence. WARNING : Sequences may be members - * of several groups. This method is incomplete. + * @return */ - SequenceGroup findGroup(SequenceI s); + SequenceGroup findGroup(SequenceI seq, int position); /** * Finds all groups that a given sequence is part of. diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index d651c0b..c467f4a 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -866,6 +866,24 @@ public class ColumnSelection */ region[0] = Math.min(region[0], start); region[1] = Math.max(region[1], end); + + /* + * also update or remove any subsequent ranges + * that are overlapped + */ + while (i < hiddenColumns.size() - 1) + { + int[] nextRegion = hiddenColumns.get(i + 1); + if (nextRegion[0] > end + 1) + { + /* + * gap to next hidden range - no more to update + */ + break; + } + region[1] = Math.max(nextRegion[1], end); + hiddenColumns.remove(i + 1); + } return; } } diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 8ee6aaf..ab3b197 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -61,9 +61,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log * @see http://rest.ensembl.org/info/rest?content-type=application/json */ - private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.8"; - private static final String LATEST_ENSEMBL_REST_VERSION = "4.7"; + private static final String LATEST_ENSEMBL_REST_VERSION = "4.8"; private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9c4ff81..370e649 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -66,6 +66,7 @@ import jalview.io.BioJsHTMLOutput; 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; @@ -131,6 +132,8 @@ 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; @@ -857,7 +860,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, modifyConservation.setEnabled(!nucleotide); 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")); @@ -1113,7 +1118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void saveAs_actionPerformed(ActionEvent e) { String format = currentFileFormat == null ? null : currentFileFormat - .toString(); + .getName(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( Cache.getProperty("LAST_DIRECTORY"), format); @@ -1147,8 +1152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1178,17 +1182,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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()) @@ -1213,15 +1206,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; @@ -1266,8 +1258,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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()) diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index df0142c..7a0b0af 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -30,7 +30,7 @@ import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SequenceI; -import jalview.io.AlignmentFileI; +import jalview.io.AlignmentFileReaderI; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormatException; @@ -73,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignViewportI viewport; - AlignmentFileI source = null; + AlignmentFileReaderI source = null; public CutAndPasteTransfer() { @@ -233,7 +233,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer if (!Jalview.isHeadlessMode()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } @@ -262,7 +262,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { String title = MessageManager.formatMessage( "label.input_cut_paste_params", - new String[] { format.toString() }); + new String[] { format.getName() }); FeatureSettingsModelI proxyColourScheme = source .getFeatureColourScheme(); @@ -340,7 +340,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer if (!Jalview.isHeadlessMode()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index ac957d8..4ce42dc 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -31,6 +31,7 @@ import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; @@ -1025,20 +1026,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - FileFormatI format = null; - FileFormatI selectedFormat = chooser.getSelectedFormat(); - if (FileFormat.Jalview.equals(selectedFormat)) - { - format = FileFormat.Jalview; - } - else + FileFormatI format = chooser.getSelectedFormat(); + + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because + * IdentifyFile does not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) { try { format = new IdentifyFile().identify(choice, DataSourceType.FILE); } catch (FileFormatException e) { - // format is null + // format = null; //?? } } diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 4f5a018..aa01bf5 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -46,8 +46,9 @@ import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; /** * DOCUMENT ME! @@ -81,6 +82,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, */ public PCAPanel(AlignmentPanel ap) { + super(); this.av = ap.av; this.ap = ap; @@ -121,6 +123,16 @@ public class PCAPanel extends GPCAPanel implements Runnable, return; } + + addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + close_actionPerformed(); + } + }); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide); PaintRefresher.Register(this, av.getSequenceSetId()); @@ -130,6 +142,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, worker.start(); } + /** + * Ensure references to potentially very large objects (the PCA matrices) are + * nulled when the frame is closed + */ + protected void close_actionPerformed() + { + pcaModel = null; + } + @Override protected void scoreMatrix_menuSelected() { diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e1b2560..e36204c 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -38,8 +38,8 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; import jalview.schemes.AnnotationColourGradient; @@ -79,7 +79,6 @@ import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPopupMenu; import javax.swing.JRadioButtonMenuItem; @@ -249,14 +248,13 @@ public class PopupMenu extends JPopupMenu colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); - colours.add(abovePIDColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); colours.add(RNAInteractionColour); - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -536,9 +534,16 @@ public class PopupMenu extends JPopupMenu noColourmenuItem.setSelected(true); } - if (sg.cs != null && sg.cs.conservationApplied()) + if (sg.cs != null) { + if (sg.cs.conservationApplied()) + { conservationMenuItem.setSelected(true); + } + if (sg.cs.getThreshold() > 0) + { + abovePIDColour.setSelected(true); + } } displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); @@ -2274,7 +2279,8 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 0b65c1b..422745a 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -701,7 +701,7 @@ public class Preferences extends GPreferences if (format != null) { Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", - format.toString()); + format.getName()); } startupFileTextfield.setText(chooser.getSelectedFile() .getAbsolutePath()); diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java index 0aa2459..00d465a 100755 --- a/src/jalview/gui/ScalePanel.java +++ b/src/jalview/gui/ScalePanel.java @@ -424,6 +424,9 @@ public class ScalePanel extends JPanel implements MouseMotionListener, { } + /** + * Creates a tooltip when the mouse is over a hidden columns marker + */ @Override public void mouseMoved(MouseEvent evt) { @@ -448,11 +451,11 @@ public class ScalePanel extends JPanel implements MouseMotionListener, ToolTipManager.sharedInstance().registerComponent(this); this.setToolTipText(MessageManager .getString("label.reveal_hidden_columns")); - break; + repaint(); + return; } } } - repaint(); } /** diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8726c4a..5b87445 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -60,7 +60,6 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.List; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -1589,19 +1588,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - stretchGroup = av.getAlignment().findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) - && (res < stretchGroup.getEndRes())) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } + stretchGroup = av.getAlignment().findGroup(sequence, res); + av.setSelectionGroup(stretchGroup); } - else if (!stretchGroup.getSequences(null).contains(sequence) + if (stretchGroup == null + || !stretchGroup.getSequences(null).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 4de510a..7333075 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -40,7 +40,8 @@ import java.util.Vector; * @author $author$ * @version $Revision$ */ -public abstract class AlignFile extends FileParse implements AlignmentFileI +public abstract class AlignFile extends FileParse implements + AlignmentFileReaderI, AlignmentFileWriterI { int noSeqs = 0; @@ -416,4 +417,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI } } + protected void addSequence(SequenceI seq) + { + seqs.add(seq); + } } diff --git a/src/jalview/io/AlignmentFileI.java b/src/jalview/io/AlignmentFileReaderI.java similarity index 69% rename from src/jalview/io/AlignmentFileI.java rename to src/jalview/io/AlignmentFileReaderI.java index 1a000a3..77a7643 100644 --- a/src/jalview/io/AlignmentFileI.java +++ b/src/jalview/io/AlignmentFileReaderI.java @@ -6,7 +6,7 @@ import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; -public interface AlignmentFileI +public interface AlignmentFileReaderI { SequenceI[] getSeqsAsArray(); @@ -15,16 +15,8 @@ public interface AlignmentFileI void addGroups(AlignmentI al); - void setNewlineString(String newline); - - void setExportSettings(AlignExportSettingI exportSettings); - - void configureForView(AlignmentViewPanel viewpanel); - void setSeqs(SequenceI[] sequencesArray); - String print(SequenceI[] seqs, boolean jvsuffix); - boolean hasWarningMessage(); String getWarningMessage(); diff --git a/src/jalview/io/AlignmentFileWriterI.java b/src/jalview/io/AlignmentFileWriterI.java new file mode 100644 index 0000000..d8e2dd4 --- /dev/null +++ b/src/jalview/io/AlignmentFileWriterI.java @@ -0,0 +1,24 @@ +package jalview.io; + +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; + +public interface AlignmentFileWriterI +{ + + void setNewlineString(String newline); + + void setExportSettings(AlignExportSettingI exportSettings); + + void configureForView(AlignmentViewPanel viewpanel); + + String print(SequenceI[] seqs, boolean jvsuffix); + + boolean hasWarningMessage(); + + String getWarningMessage(); + +} diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 45d65d6..c5a80e3 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -64,7 +64,7 @@ public class AppletFormatAdapter */ boolean serviceSecondaryStruct = false; - private AlignmentFileI alignFile = null; + private AlignmentFileReaderI alignFile = null; String inFile; @@ -77,9 +77,16 @@ public class AppletFormatAdapter public static String INVALID_CHARACTERS = "Contains invalid characters"; - public static String SUPPORTED_FORMATS = "Formats currently supported are\n" - + prettyPrint(FileFormat.getReadableFormats()); - + /** + * Returns an error message with a list of supported readable file formats + * + * @return + */ + public static String getSupportedFormats() + { + return "Formats currently supported are\n" + + prettyPrint(FileFormats.getInstance().getReadableFormats()); + } public AppletFormatAdapter() { } @@ -157,7 +164,7 @@ public class AppletFormatAdapter } else { - // todo is MCview parsing obsolete yet? + // todo is MCview parsing obsolete yet? JAL-2120 StructureImportSettings.setShowSeqFeatures(true); alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, @@ -168,7 +175,9 @@ public class AppletFormatAdapter } else { - alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + // alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + alignFile = fileFormat.getReader(new FileParse(inFile, + sourceType)); } return buildAlignmentFromFile(); } catch (Exception e) @@ -208,7 +217,7 @@ public class AppletFormatAdapter throw new IOException(e.getMessage()); } } - throw new FileFormatException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } /** @@ -248,7 +257,7 @@ public class AppletFormatAdapter } else { - alignFile = format.getAlignmentFile(source); + alignFile = format.getReader(source); } return buildAlignmentFromFile(); @@ -287,7 +296,7 @@ public class AppletFormatAdapter } // If we get to this stage, the format was not supported - throw new FileFormatException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } } @@ -361,7 +370,7 @@ public class AppletFormatAdapter { try { - AlignmentFileI afile = format.getAlignmentFile(alignment); + AlignmentFileWriterI afile = format.getWriter(alignment); afile.setNewlineString(newline); afile.setExportSettings(exportSettings); @@ -389,7 +398,8 @@ public class AppletFormatAdapter return afileresp; } catch (Exception e) { - System.err.println("Failed to write alignment as a '" + format + System.err.println("Failed to write alignment as a '" + + format.getName() + "' file\n"); e.printStackTrace(); } @@ -638,7 +648,7 @@ public class AppletFormatAdapter return null; } - public AlignmentFileI getAlignFile() + public AlignmentFileReaderI getAlignFile() { return alignFile; } diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java index 5f441d2..a11147c 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -6,31 +6,20 @@ import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; public enum FileFormat implements FileFormatI { Fasta("Fasta", "fa, fasta, mfa, fastq", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new FastaFile(inFile, sourceType); - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new FastaFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new FastaFile(); } @@ -38,21 +27,14 @@ public enum FileFormat implements FileFormatI Pfam("PFAM", "pfam", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new PfamFile(inFile, sourceType); - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PfamFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PfamFile(); } @@ -60,20 +42,14 @@ public enum FileFormat implements FileFormatI Stockholm("Stockholm", "sto,stk", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new StockholmFile(inFile, sourceType); - } - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new StockholmFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new StockholmFile(al); } @@ -83,20 +59,14 @@ public enum FileFormat implements FileFormatI PIR("PIR", "pir", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new PIRFile(inFile, sourceType); - } - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PIRFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PIRFile(); } @@ -104,19 +74,14 @@ public enum FileFormat implements FileFormatI BLC("BLC", "BLC", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new BLCFile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new BLCFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new BLCFile(); } @@ -124,21 +89,14 @@ public enum FileFormat implements FileFormatI AMSA("AMSA", "amsa", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new AMSAFile(inFile, sourceType); - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new AMSAFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new AMSAFile(al); } @@ -146,19 +104,14 @@ public enum FileFormat implements FileFormatI Html("HTML", "html", true, false) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new HtmlFile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new HtmlFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new HtmlFile(); } @@ -173,40 +126,30 @@ public enum FileFormat implements FileFormatI Rnaml("RNAML", "xml,rnaml", true, false) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new RnamlFile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new RnamlFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new RnamlFile(); } }, - Json("JSON","json", true, true) + Json("JSON", "json", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new JSONFile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new JSONFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JSONFile(); } @@ -221,19 +164,14 @@ public enum FileFormat implements FileFormatI Pileup("PileUp", "pileup", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new PileUpfile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PileUpfile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PileUpfile(); } @@ -242,19 +180,14 @@ public enum FileFormat implements FileFormatI MSF("MSF", "msf", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new MSFfile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new MSFfile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new MSFfile(); } @@ -263,19 +196,14 @@ public enum FileFormat implements FileFormatI Clustal("Clustal", "aln", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new ClustalFile(inFile, sourceType); - } @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new ClustalFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new ClustalFile(); } @@ -283,21 +211,14 @@ public enum FileFormat implements FileFormatI Phylip("PHYLIP", "phy", true, true) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new PhylipFile(inFile, sourceType); - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PhylipFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PhylipFile(); } @@ -305,16 +226,7 @@ public enum FileFormat implements FileFormatI Jnet("JnetFile", "", false, false) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - JPredFile af = new JPredFile(inFile, sourceType); - af.removeNonSequences(); - return af; - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { JPredFile af = new JPredFile(source); @@ -323,7 +235,7 @@ public enum FileFormat implements FileFormatI } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return null; // todo is this called? } @@ -332,54 +244,22 @@ public enum FileFormat implements FileFormatI Features("GFF or Jalview features", "gff2,gff3", true, false) { @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new FeaturesFile(true, inFile, sourceType); - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new FeaturesFile(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new FeaturesFile(); } }, PDB("PDB", "pdb,ent", true, false) { - - @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - // TODO obtain config value from preference settings. - // Set value to 'true' to test PDB processing with Jmol: JAL-1213 - boolean isParseWithJMOL = StructureImportSettings - .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; - if (isParseWithJMOL) - { - return new JmolParser(inFile, sourceType); - } - else - { - StructureImportSettings.setShowSeqFeatures(true); - return new MCview.PDBfile( - StructureImportSettings.isVisibleChainAnnotation(), - StructureImportSettings.isProcessSecondaryStructure(), - StructureImportSettings.isExternalSecondaryStructure(), - inFile, - sourceType); - } - } - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { boolean isParseWithJMOL = StructureImportSettings @@ -400,7 +280,7 @@ public enum FileFormat implements FileFormatI } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @@ -413,23 +293,15 @@ public enum FileFormat implements FileFormatI }, MMCif("mmCIF", "cif", true, false) { - - @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return new JmolParser(inFile, sourceType); - } - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new JmolParser(source); } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @@ -442,23 +314,15 @@ public enum FileFormat implements FileFormatI }, Jalview("Jalview", "jar,jvp", true, true) { - @Override - public AlignmentFileI getAlignmentFile(String inFile, - DataSourceType sourceType) throws IOException - { - return null; - } - - @Override - public AlignmentFileI getAlignmentFile(FileParse source) + public AlignmentFileReaderI getReader(FileParse source) throws IOException { return null; } @Override - public AlignmentFileI getAlignmentFile(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return null; } @@ -468,20 +332,13 @@ public enum FileFormat implements FileFormatI { return false; } - }; - /** - * A lookup map of enums by upper-cased name - */ - private static Map names; - static - { - names = new HashMap(); - for (FileFormat format : FileFormat.values()) + @Override + public boolean isIdentifiable() { - names.put(format.toString().toUpperCase(), format); + return false; } - } + }; private boolean writable; @@ -491,65 +348,12 @@ public enum FileFormat implements FileFormatI private String name; - /** - * Answers a list of writeable file formats (as string, corresponding to the - * toString() and forName() methods) - * - * @return - */ - public static List getWritableFormats(boolean textOnly) - { - List l = new ArrayList(); - for (FileFormatI ff : values()) - { - if (ff.isWritable() && (!textOnly || ff.isTextFormat())) - { - l.add(ff.toString()); - } - } - return l; - } - - /** - * Answers a list of readable file formats (as string, corresponding to the - * toString() and forName() methods) - * - * @return - */ - public static List getReadableFormats() - { - List l = new ArrayList(); - for (FileFormatI ff : values()) - { - if (ff.isReadable()) - { - l.add(ff.toString()); - } - } - return l; - } - @Override public boolean isComplexAlignFile() { return false; } - /** - * Returns the file format with the given name, or null if format is null or - * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to - * writers of javascript. - * - * @param format - * @return - */ - public static FileFormatI forName(String format) - { - // or could store format.getShortDescription().toUpperCase() - // in order to decouple 'given name' from enum name - return format == null ? null : names.get(format.toUpperCase()); - } - @Override public boolean isReadable() { @@ -586,19 +390,17 @@ public enum FileFormat implements FileFormatI return extensions; } + /** + * Answers the display name of the file format (as for example shown in menu + * options). This name should not be locale (language) dependent. + */ @Override - public String toString() + public String getName() { return name; } @Override - public AlignmentFileI getAlignmentFile() - { - return getAlignmentFile((AlignmentI) null); - } - - @Override public boolean isTextFormat() { return true; @@ -609,4 +411,14 @@ public enum FileFormat implements FileFormatI { return false; } + + /** + * By default, answers true, indicating the format is one that can be + * identified by IdentifyFile. Formats that cannot be identified should + * override this method to return false. + */ + public boolean isIdentifiable() + { + return true; + } } diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java index 0593d1e..e6f390d 100644 --- a/src/jalview/io/FileFormatI.java +++ b/src/jalview/io/FileFormatI.java @@ -6,20 +6,19 @@ import java.io.IOException; public interface FileFormatI { + AlignmentFileReaderI getReader(FileParse source) throws IOException; - AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType) - throws IOException; - - // TODO can we get rid of one of these methods? - AlignmentFileI getAlignmentFile(FileParse source) throws IOException; - - AlignmentFileI getAlignmentFile(AlignmentI al); - - AlignmentFileI getAlignmentFile(); + AlignmentFileWriterI getWriter(AlignmentI al); boolean isComplexAlignFile(); /** + * Answers the display name of the file format (as for example shown in menu + * options). This name should not be locale (language) dependent. + */ + String getName(); + + /** * Returns a comma-separated list of file extensions associated with the * format * @@ -29,9 +28,9 @@ public interface FileFormatI /** * Answers true if the format is one that Jalview can read. This implies that - * the format provides implementations for getAlignmentFile(FileParse) and - * getAlignmentFile(String, DataSourceType) which parse the data source for - * sequence data. + * the format provides an implementation for getReader which can parse a data + * source for sequence data. Readable formats are included in the options in + * the open file dialogue. * * @return */ @@ -39,8 +38,9 @@ public interface FileFormatI /** * Answers true if the format is one that Jalview can write. This implies that - * the object returned by getAlignmentFile provides an implementation of the - * print() method. + * the object returned by getWriter provides an implementation of the print() + * method. Writable formats are included in the options in the Save As file + * dialogue, and the 'output to Textbox' option (if text format). * * @return */ @@ -55,7 +55,7 @@ public interface FileFormatI boolean isTextFormat(); /** - * Answers true if the file format is one that provides a 3D structure + * Answers true if the file format is one that provides 3D structure data * * @return */ diff --git a/src/jalview/io/FileFormats.java b/src/jalview/io/FileFormats.java new file mode 100644 index 0000000..158489e --- /dev/null +++ b/src/jalview/io/FileFormats.java @@ -0,0 +1,168 @@ +package jalview.io; + +import java.util.ArrayList; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; + +/** + * A singleton registry of alignment file formats known to Jalview. On startup, + * the 'built-in' formats are added (from the FileFormat enum). Additional + * formats can be registered (or formats deregistered) programmatically, for + * example with a Groovy script. + * + * @author gmcarstairs + * + */ +public class FileFormats +{ + private static FileFormats instance = new FileFormats(); + + /* + * A lookup map of file formats by upper-cased name + */ + private static Map formats; + + /* + * Formats in this set are capable of being identified by IdentifyFile + */ + private static Set identifiable; + + public static FileFormats getInstance() + { + return instance; + } + + /** + * Private constructor registers Jalview's built-in file formats + */ + private FileFormats() + { + reset(); + } + + /** + * Reset to just the built-in file formats packaged with Jalview. These are + * added (and will be shown in menus) in the order of their declaration in the + * FileFormat enum. + */ + public synchronized void reset() + { + formats = new LinkedHashMap(); + identifiable = new HashSet(); + for (FileFormat format : FileFormat.values()) + { + registerFileFormat(format, format.isIdentifiable()); + } + } + + /** + * Answers true if the format is one that can be identified by IdentifyFile. + * Answers false for a null value. + */ + public boolean isIdentifiable(FileFormatI f) + { + return identifiable.contains(f); + } + + /** + * Registers a file format for case-insensitive lookup by name + * + * @param format + */ + public void registerFileFormat(FileFormatI format) + { + registerFileFormat(format, false); + } + + protected void registerFileFormat(FileFormatI format, + boolean isIdentifiable) + { + String name = format.getName().toUpperCase(); + if (formats.containsKey(name)) + { + System.err.println("Overwriting file format: " + format.getName()); + } + formats.put(name, format); + if (isIdentifiable) + { + identifiable.add(format); + } + } + + /** + * Deregisters a file format so it is no longer shown in menus + * + * @param name + */ + public void deregisterFileFormat(String name) + { + FileFormatI ff = formats.remove(name.toUpperCase()); + identifiable.remove(ff); + } + + /** + * Answers a list of writeable file formats (as strings, corresponding to the + * getName() and forName() methods) + * + * @param textOnly + * if true, only text (not binary) formats are included + * @return + */ + public List getWritableFormats(boolean textOnly) + { + List l = new ArrayList(); + for (FileFormatI ff : formats.values()) + { + if (ff.isWritable() && (!textOnly || ff.isTextFormat())) + { + l.add(ff.getName()); + } + } + return l; + } + + /** + * Answers a list of readable file formats (as strings, corresponding to the + * getName() and forName() methods) + * + * @return + */ + public List getReadableFormats() + { + List l = new ArrayList(); + for (FileFormatI ff : formats.values()) + { + if (ff.isReadable()) + { + l.add(ff.getName()); + } + } + return l; + } + + /** + * Returns the file format with the given name, or null if format is null or + * invalid. This is not case-sensitive. + * + * @param format + * @return + */ + public FileFormatI forName(String format) + { + return format == null ? null : formats.get(format.toUpperCase()); + } + + /** + * Returns an iterable collection of registered file formats (in the order in + * which they were registered) + * + * @return + */ + public Iterable getFormats() + { + return formats.values(); + } +} diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3ad74c7..4f83ab1 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -53,7 +53,8 @@ public class FileLoader implements Runnable FileFormatI format; - AlignmentFileI source = null; // alternative specification of where data comes + AlignmentFileReaderI source = null; // alternative specification of where data + // comes // from @@ -160,7 +161,7 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source, + public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source, FileFormatI format) { this.source = source; @@ -237,7 +238,7 @@ public class FileLoader implements Runnable if (protocol == DataSourceType.FILE) { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); } } @@ -279,7 +280,7 @@ public class FileLoader implements Runnable Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" - + AppletFormatAdapter.SUPPORTED_FORMATS, + + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } @@ -311,27 +312,27 @@ public class FileLoader implements Runnable } else { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - try + String error = AppletFormatAdapter.getSupportedFormats(); + try + { + if (source != null) { - if (source != null) - { - // read from the provided source + // read from the provided source al = new FormatAdapter().readFromFile(source, format); - } - else - { - - // open a new source and read from it - FormatAdapter fa = new FormatAdapter(); - al = fa.readFile(file, protocol, format); - source = fa.getAlignFile(); // keep reference for later if - // necessary. - } - } catch (java.io.IOException ex) + } + else { - error = ex.getMessage(); + + // open a new source and read from it + FormatAdapter fa = new FormatAdapter(); + al = fa.readFile(file, protocol, format); + source = fa.getAlignFile(); // keep reference for later if + // necessary. } + } catch (java.io.IOException ex) + { + error = ex.getMessage(); + } if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 1dbfdef..d9dd79d 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -155,84 +155,13 @@ public class FormatAdapter extends AppletFormatAdapter */ public String formatSequences(FileFormatI format, SequenceI[] seqs) { - // - // try - // { boolean withSuffix = getCacheSuffixDefault(format); - return format.getAlignmentFile().print(seqs, withSuffix); - // null; - // - // if (format.equalsIgnoreCase("FASTA")) - // { - // afile = new FastaFile(); - // afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", - // true)); - // } - // else if (format.equalsIgnoreCase("MSF")) - // { - // afile = new MSFfile(); - // afile.addJVSuffix(jalview.bin.Cache - // .getDefault("MSF_JVSUFFIX", true)); - // } - // else if (format.equalsIgnoreCase("PileUp")) - // { - // afile = new PileUpfile(); - // afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", - // true)); - // } - // else if (format.equalsIgnoreCase("CLUSTAL")) - // { - // afile = new ClustalFile(); - // afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", - // true)); - // } - // else if (format.equalsIgnoreCase("BLC")) - // { - // afile = new BLCFile(); - // afile.addJVSuffix(jalview.bin.Cache - // .getDefault("BLC_JVSUFFIX", true)); - // } - // else if (format.equalsIgnoreCase("PIR")) - // { - // afile = new PIRFile(); - // afile.addJVSuffix(jalview.bin.Cache - // .getDefault("PIR_JVSUFFIX", true)); - // } - // else if (format.equalsIgnoreCase("PFAM")) - // { - // afile = new PfamFile(); - // afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", - // true)); - // } - // /* - // * amsa is not supported by this function - it requires an alignment - // * rather than a sequence vector else if - // (format.equalsIgnoreCase("AMSA")) - // * { afile = new AMSAFile(); afile.addJVSuffix( - // * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); } - // */ - -// afile.setSeqs(seqs); -// String afileresp = afile.print(); -// if (afile.hasWarningMessage()) -// { -// System.err.println("Warning raised when writing as " + format -// + " : " + afile.getWarningMessage()); -// } -// return afileresp; -// } catch (Exception e) -// { -// System.err.println("Failed to write alignment as a '" + format -// + "' file\n"); -// e.printStackTrace(); -// } -// -// return null; + return format.getWriter(null).print(seqs, withSuffix); } public boolean getCacheSuffixDefault(FileFormatI format) { - return Cache.getDefault(format.toString() + "_JVSUFFIX", true); + return Cache.getDefault(format.getName() + "_JVSUFFIX", true); } public String formatSequences(FileFormatI format, AlignmentI alignment, @@ -329,8 +258,8 @@ public class FormatAdapter extends AppletFormatAdapter selectedOnly); } - public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format) - throws IOException + public AlignmentI readFromFile(AlignmentFileReaderI source, + FileFormatI format) throws IOException { FileParse fp = new FileParse(source.getInFile(), source.getDataSourceType()); diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 72a1155..0556e76 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -72,7 +72,7 @@ public class IdentifyFile // preserves original behaviour prior to version 2.3 } - public FileFormatI identify(AlignmentFileI file, boolean closeSource) + public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource) throws IOException { FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType()); diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index 7ccdaa9..2a0f8b1 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -68,12 +68,12 @@ public class JalviewFileChooser extends JFileChooser { List extensions = new ArrayList(); List descs = new ArrayList(); - for (FileFormatI format : FileFormat.values()) + for (FileFormatI format : FileFormats.getInstance().getFormats()) { if (format.isReadable()) { extensions.add(format.getExtensions()); - descs.add(format.toString()); + descs.add(format.getName()); } } return new JalviewFileChooser(directory, @@ -96,12 +96,12 @@ public class JalviewFileChooser extends JFileChooser // with a lambda expression parameter for isReadable/isWritable List extensions = new ArrayList(); List descs = new ArrayList(); - for (FileFormatI format : FileFormat.values()) + for (FileFormatI format : FileFormats.getInstance().getFormats()) { if (format.isWritable()) { extensions.add(format.getExtensions()); - descs.add(format.toString()); + descs.add(format.getName()); } } return new JalviewFileChooser(directory, @@ -269,7 +269,7 @@ public class JalviewFileChooser extends JFileChooser format = format.substring(0, parenPos).trim(); try { - return FileFormat.valueOf(format); + return FileFormats.getInstance().forName(format); } catch (IllegalArgumentException e) { System.err.println("Unexpected format: " + format); diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java index 3461110..6bfb3b9 100755 --- a/src/jalview/io/JalviewFileView.java +++ b/src/jalview/io/JalviewFileView.java @@ -38,9 +38,9 @@ public class JalviewFileView extends FileView private void loadExtensions() { extensions = new HashMap(); - for (FileFormatI ff : FileFormat.values()) + for (FileFormatI ff : FileFormats.getInstance().getFormats()) { - String desc = ff.toString() + " file"; + String desc = ff.getName() + " file"; String exts = ff.getExtensions(); for (String ext : exts.split(",")) { diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 4de3d3a..dc17397 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -26,7 +26,7 @@ import jalview.bin.Cache; import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; -import jalview.io.FileFormat; +import jalview.io.FileFormats; import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; @@ -245,7 +245,7 @@ public class GAlignFrame extends JInternalFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -2319,7 +2319,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(purinePyrimidineColour); - colourMenu.add(RNAInteractionColour); + // colourMenu.add(RNAInteractionColour); // colourMenu.add(covariationColour); colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index bb7ed37..28b9d67 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -57,24 +57,33 @@ public class Matrix int maxIter = 45; // fudge - add 15 iterations, just in case /** - * Creates a new Matrix object. + * Creates a new Matrix object. For example * - * @param value - * DOCUMENT ME! + *
+ * new Matrix(new double[][] {{2, 3}, {4, 5}, 2, 2) + * constructs + * (2 3) + * (4 5) + *
+ * + * Note that ragged arrays (with not all rows, or columns, of the same + * length), are not supported by this class. They can be constructed, but + * results of operations on them are undefined and may throw exceptions. + * + * @param values + * the matrix values in row-major order * @param rows - * DOCUMENT ME! * @param cols - * DOCUMENT ME! */ - public Matrix(double[][] value, int rows, int cols) + public Matrix(double[][] values, int rows, int cols) { this.rows = rows; this.cols = cols; - this.value = value; + this.value = values; } /** - * DOCUMENT ME! + * Returns a new matrix which is the transposes of this one * * @return DOCUMENT ME! */ @@ -113,15 +122,24 @@ public class Matrix } /** - * DOCUMENT ME! + * Returns a new matrix which is the result of premultiplying this matrix by + * the supplied argument. If this of size AxB (A rows and B columns), and the + * argument is CxA (C rows and A columns), the result is of size CxB. * * @param in - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return + * @throws IllegalArgumentException + * if the number of columns in the pre-multiplier is not equal to + * the number of rows in the multiplicand (this) */ public Matrix preMultiply(Matrix in) { + if (in.cols != this.rows) + { + throw new IllegalArgumentException("Can't pre-multiply " + this.rows + + " rows by " + in.cols + " columns"); + } double[][] tmp = new double[in.rows][this.cols]; for (int i = 0; i < in.rows; i++) @@ -141,12 +159,10 @@ public class Matrix } /** - * DOCUMENT ME! * * @param in - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return */ public double[] vectorPostMultiply(double[] in) { @@ -166,37 +182,34 @@ public class Matrix } /** - * DOCUMENT ME! + * Returns a new matrix which is the result of postmultiplying this matrix by + * the supplied argument. If this of size AxB (A rows and B columns), and the + * argument is BxC (B rows and C columns), the result is of size AxC. + *
+ * This method simply returns the result of in.preMultiply(this) * * @param in - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return + * @throws IllegalArgumentException + * if the number of rows in the post-multiplier is not equal to the + * number of columns in the multiplicand (this) + * @see #preMultiply(Matrix) */ public Matrix postMultiply(Matrix in) { - double[][] out = new double[this.rows][in.cols]; - - for (int i = 0; i < this.rows; i++) + if (in.rows != this.cols) { - for (int j = 0; j < in.cols; j++) - { - out[i][j] = 0.0; - - for (int k = 0; k < rows; k++) - { - out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]); - } - } + throw new IllegalArgumentException("Can't post-multiply " + this.cols + + " columns by " + in.rows + " rows"); } - - return new Matrix(out, this.cols, in.rows); + return in.preMultiply(this); } /** - * DOCUMENT ME! + * Answers a new matrix with a copy of the values in this one * - * @return DOCUMENT ME! + * @return */ public Matrix copy() { @@ -204,10 +217,11 @@ public class Matrix for (int i = 0; i < rows; i++) { - for (int j = 0; j < cols; j++) - { - newmat[i][j] = value[i][j]; - } + System.arraycopy(value[i], 0, newmat[i], 0, value[i].length); + // for (int j = 0; j < cols; j++) + // { + // newmat[i][j] = value[i][j]; + // } } return new Matrix(newmat, rows, cols); @@ -738,20 +752,19 @@ public class Matrix } /** - * DOCUMENT ME! + * Returns an array containing the values in the specified column * - * @param n - * DOCUMENT ME! + * @param col * - * @return DOCUMENT ME! + * @return */ - public double[] getColumn(int n) + public double[] getColumn(int col) { double[] out = new double[rows]; for (int i = 0; i < rows; i++) { - out[i] = value[i][n]; + out[i] = value[i][col]; } return out; @@ -784,85 +797,4 @@ public class Matrix Format.print(ps, "%15.4e", e[j]); } } - - /** - * DOCUMENT ME! - * - * @param args - * DOCUMENT ME! - */ - public static void main(String[] args) throws Exception - { - int n = Integer.parseInt(args[0]); - double[][] in = new double[n][n]; - - for (int i = 0; i < n; i++) - { - for (int j = 0; j < n; j++) - { - in[i][j] = (double) Math.random(); - } - } - - Matrix origmat = new Matrix(in, n, n); - - // System.out.println(" --- Original matrix ---- "); - // / origmat.print(System.out); - // System.out.println(); - // System.out.println(" --- transpose matrix ---- "); - Matrix trans = origmat.transpose(); - - // trans.print(System.out); - // System.out.println(); - // System.out.println(" --- OrigT * Orig ---- "); - Matrix symm = trans.postMultiply(origmat); - - // symm.print(System.out); - // System.out.println(); - // Copy the symmetric matrix for later - // Matrix origsymm = symm.copy(); - - // This produces the tridiagonal transformation matrix - // long tstart = System.currentTimeMillis(); - symm.tred(); - - // long tend = System.currentTimeMillis(); - - // System.out.println("Time take for tred = " + (tend-tstart) + "ms"); - // System.out.println(" ---Tridiag transform matrix ---"); - // symm.print(System.out); - // System.out.println(); - // System.out.println(" --- D vector ---"); - // symm.printD(System.out); - // System.out.println(); - // System.out.println(" --- E vector ---"); - // symm.printE(System.out); - // System.out.println(); - // Now produce the diagonalization matrix - // tstart = System.currentTimeMillis(); - symm.tqli(); - // tend = System.currentTimeMillis(); - - // System.out.println("Time take for tqli = " + (tend-tstart) + " ms"); - // System.out.println(" --- New diagonalization matrix ---"); - // symm.print(System.out); - // System.out.println(); - // System.out.println(" --- D vector ---"); - // symm.printD(System.out); - // System.out.println(); - // System.out.println(" --- E vector ---"); - // symm.printE(System.out); - // System.out.println(); - // System.out.println(" --- First eigenvector --- "); - // double[] eigenv = symm.getColumn(0); - // for (int i=0; i < eigenv.length;i++) { - // Format.print(System.out,"%15.4f",eigenv[i]); - // } - // System.out.println(); - // double[] neigenv = origsymm.vectorPostMultiply(eigenv); - // for (int i=0; i < neigenv.length;i++) { - // Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]); - // } - // System.out.println(); - } } diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java index 389afcd..bf52027 100755 --- a/src/jalview/util/Format.java +++ b/src/jalview/util/Format.java @@ -884,21 +884,18 @@ public class Format String f = ""; int e = 0; double dd = d; - double factor = 1; if (d != 0) { while (dd > 10) { e++; - factor /= 10; dd = dd / 10; } while (dd < 1) { e--; - factor *= 10; dd = dd * 10; } } @@ -908,8 +905,7 @@ public class Format return fixed_format(d); } - d = d * factor; - f = f + fixed_format(d); + f = f + fixed_format(dd); if ((fmt == 'e') || (fmt == 'g')) { diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 7258f51..ba4054e 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -222,7 +222,7 @@ public class Discoverer implements Runnable + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" + "\ndoi://10.1093/nar/gkv332", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JNet Secondary Structure Prediction") }; + "JPred Secondary Structure Prediction") }; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java index 2c05386..65847e6 100644 --- a/src/jalview/ws/jws1/JPredClient.java +++ b/src/jalview/ws/jws1/JPredClient.java @@ -238,7 +238,7 @@ public class JPredClient extends WS1Client SequenceI seq = msf[0]; - String altitle = "JNet prediction on " + seq.getName() + String altitle = "JPred prediction on " + seq.getName() + " using alignment from " + title; wsInfo.setProgressText("Job details for MSA based prediction (" + title @@ -275,7 +275,7 @@ public class JPredClient extends WS1Client wsInfo.setProgressText("Job details for prediction on sequence :\n>" + seq.getName() + "\n" + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n"); - String altitle = "JNet prediction for sequence " + seq.getName() + String altitle = "JPred prediction for sequence " + seq.getName() + " from " + title; Hashtable SequenceInfo = jalview.analysis.SeqsetUtils diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 4e5cadc..e685d00 100644 --- a/src/jalview/ws/jws1/JPredThread.java +++ b/src/jalview/ws/jws1/JPredThread.java @@ -180,8 +180,8 @@ class JPredThread extends JWS1Thread implements WSClientI else { throw (new Exception(MessageManager.formatMessage( - "exception.unknown_format_for_file", new String[] { - format.toString(), result.getAligfile() }))); + "exception.unknown_format_for_file", new String[] { "", + result.getAligfile() }))); } } else diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java index 08a242d..a8258e2 100644 --- a/src/jalview/ws/rest/params/Alignment.java +++ b/src/jalview/ws/rest/params/Alignment.java @@ -23,6 +23,7 @@ package jalview.ws.rest.params; import jalview.datamodel.AlignmentI; import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FormatAdapter; import jalview.ws.params.OptionI; import jalview.ws.params.simple.BooleanOption; @@ -147,9 +148,9 @@ public class Alignment extends InputType if (tok.startsWith("format")) { - for (FileFormatI fmt : FileFormat.values()) + for (FileFormatI fmt : FileFormats.getInstance().getFormats()) { - if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString())) + if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName())) { format = fmt; return true; @@ -157,12 +158,9 @@ public class Alignment extends InputType } warnings.append("Invalid alignment format '" + val + "'. Must be one of ("); - for (FileFormatI fmt : FileFormat.values()) + for (String fmt : FileFormats.getInstance().getWritableFormats(true)) { - if (fmt.isWritable()) - { - warnings.append(" " + fmt).toString(); - } + warnings.append(" ").append(fmt); } warnings.append(")\n"); } @@ -197,28 +195,14 @@ public class Alignment extends InputType "Append jalview style /start-end suffix to ID", false, false, writeAsFile, null)); + List writable = FileFormats + .getInstance().getWritableFormats(true); lst.add(new Option("format", "Alignment upload format", true, - FileFormat.Fasta.toString(), format.toString(), getWritableFormats(), + FileFormat.Fasta.toString(), format.getName(), writable, null)); lst.add(createMolTypeOption("type", "Sequence type", false, type, null)); return lst; } - /** - * @return - */ - protected List getWritableFormats() - { - List formats = new ArrayList(); - for (FileFormatI ff : FileFormat.values()) - { - if (ff.isWritable()) - { - formats.add(ff.toString()); - } - } - return formats; - } - } diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 37388d3..ea65125 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -295,6 +295,7 @@ public class SiftsClient implements SiftsClientI siftsDownloadDir.mkdirs(); } // System.out.println(">> Download ftp url : " + siftsFileFTPURL); + // long now = System.currentTimeMillis(); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); InputStream inputStream = conn.getInputStream(); @@ -308,7 +309,8 @@ public class SiftsClient implements SiftsClientI } outputStream.close(); inputStream.close(); - // System.out.println(">>> File downloaded : " + downloadedSiftsFile); +// System.out.println(">>> File downloaded : " + downloadedSiftsFile +// + " took " + (System.currentTimeMillis() - now) + "ms"); return new File(downloadedSiftsFile); } diff --git a/test/jalview/analysis/DnaAlignmentGenerator.java b/test/jalview/analysis/AlignmentGenerator.java similarity index 82% rename from test/jalview/analysis/DnaAlignmentGenerator.java rename to test/jalview/analysis/AlignmentGenerator.java index 60dd929..3187fd9 100644 --- a/test/jalview/analysis/DnaAlignmentGenerator.java +++ b/test/jalview/analysis/AlignmentGenerator.java @@ -51,9 +51,8 @@ import org.testng.annotations.BeforeClass; * @author gmcarstairs * */ -public class DnaAlignmentGenerator +public class AlignmentGenerator { - @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { @@ -65,7 +64,11 @@ public class DnaAlignmentGenerator private static final char ZERO = '0'; - private static final char[] BASES = new char[] { 'G', 'T', 'C', 'A' }; + private static final char[] NUCS = "GTCA".toCharArray(); + + private static final char[] PEPS = "MILVFYWHKRDEQNTCGASNP".toCharArray(); + + private static char[] BASES; private Random random; @@ -78,17 +81,19 @@ public class DnaAlignmentGenerator */ public static void main(String[] args) { - if (args.length != 5) + if (args.length != 6) { usage(); return; } - int width = Integer.parseInt(args[0]); - int height = Integer.parseInt(args[1]); - long randomSeed = Long.valueOf(args[2]); - int gapPercentage = Integer.valueOf(args[3]); - int changePercentage = Integer.valueOf(args[4]); - AlignmentI al = new DnaAlignmentGenerator().generate(width, height, + boolean nucleotide = args[0].toLowerCase().startsWith("n"); + int width = Integer.parseInt(args[1]); + int height = Integer.parseInt(args[2]); + long randomSeed = Long.valueOf(args[3]); + int gapPercentage = Integer.valueOf(args[4]); + int changePercentage = Integer.valueOf(args[5]); + AlignmentI al = new AlignmentGenerator(nucleotide).generate(width, + height, randomSeed, gapPercentage, changePercentage); System.out.println("; " + height + " sequences of " + width @@ -104,25 +109,26 @@ public class DnaAlignmentGenerator private static void usage() { System.out.println("Usage:"); - System.out.println("arg0: number of (non-gap) bases per sequence"); - System.out.println("arg1: number sequences"); + System.out.println("arg0: n (for nucleotide) or p (for peptide)"); + System.out.println("arg1: number of (non-gap) bases per sequence"); + System.out.println("arg2: number sequences"); System.out - .println("arg2: an integer as random seed (same seed = same results)"); - System.out.println("arg3: percentage of gaps to (randomly) generate"); + .println("arg3: an integer as random seed (same seed = same results)"); + System.out.println("arg4: percentage of gaps to (randomly) generate"); System.out - .println("arg4: percentage of 'mutations' to (randomly) generate"); - System.out.println("Example: DnaAlignmentGenerator 12 15 387 10 5"); + .println("arg5: percentage of 'mutations' to (randomly) generate"); + System.out.println("Example: AlignmentGenerator n 12 15 387 10 5"); System.out - .println("- 15 sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387"); + .println("- 15 nucleotide sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387"); } /** - * Default constructor + * Constructor that sets nucleotide or peptide symbol set */ - public DnaAlignmentGenerator() + public AlignmentGenerator(boolean nuc) { - + BASES = nuc ? NUCS : PEPS; } /** @@ -168,7 +174,8 @@ public class DnaAlignmentGenerator for (int count = 0; count < length;) { boolean addGap = random.nextInt(100) < gapPercentage; - char c = addGap ? GAP : BASES[random.nextInt(Integer.MAX_VALUE) % 4]; + char c = addGap ? GAP : BASES[random.nextInt(Integer.MAX_VALUE) + % BASES.length]; seq.append(c); if (!addGap) { @@ -277,7 +284,7 @@ public class DnaAlignmentGenerator char newchar = c; while (newchar == c) { - newchar = BASES[random.nextInt(Integer.MAX_VALUE) % 4]; + newchar = BASES[random.nextInt(Integer.MAX_VALUE) % BASES.length]; } return newchar; } diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index cd5d3ca..2e21d9c 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -294,7 +294,8 @@ public class DnaTest /* * Generate cDNA - 8 sequences of 12 bases each. */ - AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5); + AlignmentI cdna = new AlignmentGenerator(true) + .generate(12, 8, 97, 5, 5); ColumnSelection cs = new ColumnSelection(); AlignViewportI av = new AlignViewport(cdna, cs); Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 }); diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index d2f4b4d..618bac5 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -1131,4 +1131,63 @@ public class AlignmentTest assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to); } + @Test(groups = { "Functional" }) + public void testFindGroup() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI"); + SequenceI seq2 = new Sequence("seq2", "---JKLMNO---"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 }); + + assertNull(a.findGroup(null, 0)); + assertNull(a.findGroup(seq1, 1)); + assertNull(a.findGroup(seq1, -1)); + + /* + * add a group consisting of just "DEF" + */ + SequenceGroup sg1 = new SequenceGroup(); + sg1.addSequence(seq1, false); + sg1.setStartRes(3); + sg1.setEndRes(5); + a.addGroup(sg1); + + assertNull(a.findGroup(seq1, 2)); // position not in group + assertNull(a.findGroup(seq1, 6)); // position not in group + assertNull(a.findGroup(seq2, 5)); // sequence not in group + assertSame(a.findGroup(seq1, 3), sg1); // yes + assertSame(a.findGroup(seq1, 4), sg1); + assertSame(a.findGroup(seq1, 5), sg1); + + /* + * add a group consisting of + * EF-- + * KLMN + */ + SequenceGroup sg2 = new SequenceGroup(); + sg2.addSequence(seq1, false); + sg2.addSequence(seq2, false); + sg2.setStartRes(4); + sg2.setEndRes(7); + a.addGroup(sg2); + + assertNull(a.findGroup(seq1, 2)); // unchanged + assertSame(a.findGroup(seq1, 3), sg1); // unchanged + /* + * if a residue is in more than one group, method returns + * the first found (in order groups were added) + */ + assertSame(a.findGroup(seq1, 4), sg1); + assertSame(a.findGroup(seq1, 5), sg1); + + /* + * seq2 only belongs to the second group + */ + assertSame(a.findGroup(seq2, 4), sg2); + assertSame(a.findGroup(seq2, 5), sg2); + assertSame(a.findGroup(seq2, 6), sg2); + assertSame(a.findGroup(seq2, 7), sg2); + assertNull(a.findGroup(seq2, 3)); + assertNull(a.findGroup(seq2, 8)); + } + } diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java index a9ad4c2..4faa482 100644 --- a/test/jalview/datamodel/ColumnSelectionTest.java +++ b/test/jalview/datamodel/ColumnSelectionTest.java @@ -205,12 +205,11 @@ public class ColumnSelectionTest assertEquals("[5, 5]", Arrays.toString(hidden.get(1))); // hiding column 4 expands [3, 3] to [3, 4] - // not fancy enough to coalesce this into [3, 5] though + // and merges to [5, 5] to make [3, 5] cs.hideColumns(4); hidden = cs.getHiddenColumns(); - assertEquals(2, hidden.size()); - assertEquals("[3, 4]", Arrays.toString(hidden.get(0))); - assertEquals("[5, 5]", Arrays.toString(hidden.get(1))); + assertEquals(1, hidden.size()); + assertEquals("[3, 5]", Arrays.toString(hidden.get(0))); // clear hidden columns (note they are added to selected) cs.revealAllHiddenColumns(); @@ -761,4 +760,59 @@ public class ColumnSelectionTest assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0))); assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1))); } + + /** + * Test for the case when a hidden range encloses more one already hidden + * range + */ + @Test(groups = { "Functional" }) + public void testHideColumns_subsumingHidden() + { + /* + * JAL-2370 bug scenario: + * two hidden ranges subsumed by a third + */ + ColumnSelection cs = new ColumnSelection(); + cs.hideColumns(49, 59); + cs.hideColumns(69, 79); + List hidden = cs.getHiddenColumns(); + assertEquals(2, hidden.size()); + assertEquals("[49, 59]", Arrays.toString(hidden.get(0))); + assertEquals("[69, 79]", Arrays.toString(hidden.get(1))); + + cs.hideColumns(48, 80); + hidden = cs.getHiddenColumns(); + assertEquals(1, hidden.size()); + assertEquals("[48, 80]", Arrays.toString(hidden.get(0))); + + /* + * another...joining hidden ranges + */ + cs = new ColumnSelection(); + cs.hideColumns(10, 20); + cs.hideColumns(30, 40); + cs.hideColumns(50, 60); + // hiding 21-49 should merge to one range + cs.hideColumns(21, 49); + hidden = cs.getHiddenColumns(); + assertEquals(1, hidden.size()); + assertEquals("[10, 60]", Arrays.toString(hidden.get(0))); + + /* + * another...lef overlap, subsumption, right overlap, + * no overlap of existing hidden ranges + */ + cs = new ColumnSelection(); + cs.hideColumns(10, 20); + cs.hideColumns(10, 20); + cs.hideColumns(30, 35); + cs.hideColumns(40, 50); + cs.hideColumns(60, 70); + + cs.hideColumns(15, 45); + hidden = cs.getHiddenColumns(); + assertEquals(2, hidden.size()); + assertEquals("[10, 50]", Arrays.toString(hidden.get(0))); + assertEquals("[60, 70]", Arrays.toString(hidden.get(1))); + } } diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java new file mode 100644 index 0000000..8df228f --- /dev/null +++ b/test/jalview/io/FileFormatsTest.java @@ -0,0 +1,156 @@ +package jalview.io; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotEquals; +import static org.testng.Assert.assertNull; +import static org.testng.Assert.assertSame; +import static org.testng.Assert.assertTrue; + +import java.util.Iterator; + +import org.testng.annotations.AfterMethod; +import org.testng.annotations.Test; + +public class FileFormatsTest +{ + @AfterMethod() + public void tearDown() + { + FileFormats.getInstance().reset(); + } + + @Test(groups = "Functional") + public void testIsDynamic() + { + FileFormats formats = FileFormats.getInstance(); + for (FileFormatI ff : FileFormat.values()) + { + assertFalse(formats.isIdentifiable(ff)); + } + assertTrue(formats.isIdentifiable(null)); + + /* + * remove and re-add a format: it is now considered 'dynamically added' + */ + formats.deregisterFileFormat(FileFormat.Fasta.getName()); + assertNull(formats.forName(FileFormat.Fasta.getName())); + formats.registerFileFormat(FileFormat.Fasta); + assertSame(FileFormat.Fasta, + formats.forName(FileFormat.Fasta.getName())); + assertTrue(formats.isIdentifiable(FileFormat.Fasta)); + } + + @Test(groups = "Functional") + public void testGetReadableFormats() + { + String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]"; + FileFormats formats = FileFormats.getInstance(); + assertEquals(formats.getReadableFormats().toString(), expected); + } + + @Test(groups = "Functional") + public void testGetWritableFormats() + { + String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]"; + FileFormats formats = FileFormats.getInstance(); + assertEquals(formats.getWritableFormats(true).toString(), expected); + expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]"; + assertEquals(formats.getWritableFormats(false).toString(), expected); + } + + @Test(groups = "Functional") + public void testDeregisterFileFormat() + { + String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]"; + String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]"; + FileFormats formats = FileFormats.getInstance(); + assertEquals(formats.getWritableFormats(true).toString(), writable); + assertEquals(formats.getReadableFormats().toString(), readable); + + formats.deregisterFileFormat(FileFormat.Fasta.getName()); + writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]"; + readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]"; + assertEquals(formats.getWritableFormats(true).toString(), writable); + assertEquals(formats.getReadableFormats().toString(), readable); + + /* + * re-register the format: it gets added to the end of the list + */ + formats.registerFileFormat(FileFormat.Fasta); + writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]"; + readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]"; + assertEquals(formats.getWritableFormats(true).toString(), writable); + assertEquals(formats.getReadableFormats().toString(), readable); + } + + @Test(groups = "Functional") + public void testForName() + { + FileFormats formats = FileFormats.getInstance(); + for (FileFormatI ff : FileFormat.values()) + { + assertSame(ff, formats.forName(ff.getName())); + assertSame(ff, formats.forName(ff.getName().toUpperCase())); + assertSame(ff, formats.forName(ff.getName().toLowerCase())); + } + assertNull(formats.forName(null)); + assertNull(formats.forName("rubbish")); + } + + @Test(groups = "Functional") + public void testRegisterFileFormat() + { + FileFormats formats = FileFormats.getInstance(); + assertSame(FileFormat.MMCif, + formats.forName(FileFormat.MMCif.getName())); + assertFalse(formats.isIdentifiable(FileFormat.MMCif)); + + /* + * deregister mmCIF format + */ + formats.deregisterFileFormat(FileFormat.MMCif.getName()); + assertNull(formats.forName(FileFormat.MMCif.getName())); + + /* + * re-register mmCIF format + * it is reinstated (but now classed as 'dynamic') + */ + formats.registerFileFormat(FileFormat.MMCif); + assertSame(FileFormat.MMCif, + formats.forName(FileFormat.MMCif.getName())); + assertTrue(formats.isIdentifiable(FileFormat.MMCif)); + // repeating does nothing + formats.registerFileFormat(FileFormat.MMCif); + assertSame(FileFormat.MMCif, + formats.forName(FileFormat.MMCif.getName())); + } + + @Test(groups = "Functional") + public void testGetFormats() + { + /* + * verify the list of file formats registered matches the enum values + */ + FileFormats instance = FileFormats.getInstance(); + Iterator formats = instance.getFormats() + .iterator(); + FileFormatI[] builtIn = FileFormat.values(); + + for (FileFormatI ff : builtIn) + { + assertSame(ff, formats.next()); + } + assertFalse(formats.hasNext()); + + /* + * remove the first format, check it is no longer in + * the list of formats + */ + String firstFormatName = instance.getFormats().iterator().next() + .getName(); + instance.deregisterFileFormat(firstFormatName); + assertNotEquals(instance.getFormats().iterator().next().getName(), + firstFormatName); + } +} diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java index 7aa5769..b500266 100644 --- a/test/jalview/io/FormatAdapterTest.java +++ b/test/jalview/io/FormatAdapterTest.java @@ -132,7 +132,7 @@ public class FormatAdapterTest static Object[][] getFormats() { List both = new ArrayList(); - for (FileFormat format : FileFormat.values()) + for (FileFormatI format : FileFormats.getInstance().getFormats()) { if (format.isReadable() && format.isWritable() && format.isTextFormat()) diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java new file mode 100644 index 0000000..795b2fa --- /dev/null +++ b/test/jalview/math/MatrixTest.java @@ -0,0 +1,239 @@ +package jalview.math; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.fail; + +import java.util.Arrays; + +import org.testng.annotations.Test; + +public class MatrixTest +{ + @Test(groups = "Timing") + public void testPreMultiply_timing() + { + int rows = 500; + int cols = 1000; + double[][] d1 = new double[rows][cols]; + double[][] d2 = new double[cols][rows]; + Matrix m1 = new Matrix(d1, rows, cols); + Matrix m2 = new Matrix(d2, cols, rows); + long start = System.currentTimeMillis(); + m1.preMultiply(m2); + long elapsed = System.currentTimeMillis() - start; + System.out.println(rows + "x" + cols + + " multiplications of double took " + elapsed + "ms"); + } + + @Test(groups = "Functional") + public void testPreMultiply() + { + Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 } }, 1, 3); // 1x3 + Matrix m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }, 3, 1); // 3x1 + + /* + * 1x3 times 3x1 is 1x1 + * 2x5 + 3x6 + 4*7 = 56 + */ + Matrix m3 = m2.preMultiply(m1); + assertEquals(m3.rows, 1); + assertEquals(m3.cols, 1); + assertEquals(m3.value[0][0], 56d); + + /* + * 3x1 times 1x3 is 3x3 + */ + m3 = m1.preMultiply(m2); + assertEquals(m3.rows, 3); + assertEquals(m3.cols, 3); + assertEquals(Arrays.toString(m3.value[0]), "[10.0, 15.0, 20.0]"); + assertEquals(Arrays.toString(m3.value[1]), "[12.0, 18.0, 24.0]"); + assertEquals(Arrays.toString(m3.value[2]), "[14.0, 21.0, 28.0]"); + } + + @Test( + groups = "Functional", + expectedExceptions = { IllegalArgumentException.class }) + public void testPreMultiply_tooManyColumns() + { + Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }, 2, + 3); // 2x3 + + /* + * 2x3 times 2x3 invalid operation - + * multiplier has more columns than multiplicand has rows + */ + m1.preMultiply(m1); + fail("Expected exception"); + } + + @Test( + groups = "Functional", + expectedExceptions = { IllegalArgumentException.class }) + public void testPreMultiply_tooFewColumns() + { + Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }, 2, + 3); // 2x3 + + /* + * 3x2 times 3x2 invalid operation - + * multiplier has more columns than multiplicand has row + */ + m1.preMultiply(m1); + fail("Expected exception"); + } + + + private boolean matrixEquals(Matrix m1, Matrix m2) { + return Arrays.deepEquals(m1.value, m2.value); + } + + @Test(groups = "Functional") + public void testPostMultiply() + { + /* + * Square matrices + * (2 3) . (10 100) + * (4 5) (1000 10000) + * = + * (3020 30200) + * (5040 50400) + */ + Matrix m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } }, 2, 2); + Matrix m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } }, + 2, 2); + Matrix m3 = m1.postMultiply(m2); + assertEquals(Arrays.toString(m3.value[0]), "[3020.0, 30200.0]"); + assertEquals(Arrays.toString(m3.value[1]), "[5040.0, 50400.0]"); + + /* + * also check m2.preMultiply(m1) - should be same as m1.postMultiply(m2) + */ + m3 = m2.preMultiply(m1); + assertEquals(Arrays.toString(m3.value[0]), "[3020.0, 30200.0]"); + assertEquals(Arrays.toString(m3.value[1]), "[5040.0, 50400.0]"); + + /* + * m1 has more rows than columns + * (2).(10 100 1000) = (20 200 2000) + * (3) (30 300 3000) + */ + m1 = new Matrix(new double[][] { { 2 }, { 3 } }, 2, 1); + m2 = new Matrix(new double[][] { { 10, 100, 1000 } }, 1, 3); + m3 = m1.postMultiply(m2); + assertEquals(m3.rows, 2); + assertEquals(m3.cols, 3); + assertEquals(Arrays.toString(m3.value[0]), "[20.0, 200.0, 2000.0]"); + assertEquals(Arrays.toString(m3.value[1]), "[30.0, 300.0, 3000.0]"); + m3 = m2.preMultiply(m1); + assertEquals(m3.rows, 2); + assertEquals(m3.cols, 3); + assertEquals(Arrays.toString(m3.value[0]), "[20.0, 200.0, 2000.0]"); + assertEquals(Arrays.toString(m3.value[1]), "[30.0, 300.0, 3000.0]"); + + /* + * m1 has more columns than rows + * (2 3 4) . (5 4) = (56 25) + * (6 3) + * (7 2) + * [0, 0] = 2*5 + 3*6 + 4*7 = 56 + * [0, 1] = 2*4 + 3*3 + 4*2 = 25 + */ + m1 = new Matrix(new double[][] { { 2, 3, 4 } }, 1, 3); + m2 = new Matrix(new double[][] { { 5, 4 }, { 6, 3 }, { 7, 2 } }, 3, 2); + m3 = m1.postMultiply(m2); + assertEquals(m3.rows, 1); + assertEquals(m3.cols, 2); + assertEquals(m3.value[0][0], 56d); + assertEquals(m3.value[0][1], 25d); + + /* + * and check premultiply equivalent + */ + m3 = m2.preMultiply(m1); + assertEquals(m3.rows, 1); + assertEquals(m3.cols, 2); + assertEquals(m3.value[0][0], 56d); + assertEquals(m3.value[0][1], 25d); + } + + /** + * main method extracted from Matrix + * + * @param args + */ + public static void main(String[] args) throws Exception + { + int n = Integer.parseInt(args[0]); + double[][] in = new double[n][n]; + + for (int i = 0; i < n; i++) + { + for (int j = 0; j < n; j++) + { + in[i][j] = Math.random(); + } + } + + Matrix origmat = new Matrix(in, n, n); + + // System.out.println(" --- Original matrix ---- "); + // / origmat.print(System.out); + // System.out.println(); + // System.out.println(" --- transpose matrix ---- "); + Matrix trans = origmat.transpose(); + + // trans.print(System.out); + // System.out.println(); + // System.out.println(" --- OrigT * Orig ---- "); + Matrix symm = trans.postMultiply(origmat); + + // symm.print(System.out); + // System.out.println(); + // Copy the symmetric matrix for later + // Matrix origsymm = symm.copy(); + + // This produces the tridiagonal transformation matrix + // long tstart = System.currentTimeMillis(); + symm.tred(); + + // long tend = System.currentTimeMillis(); + + // System.out.println("Time take for tred = " + (tend-tstart) + "ms"); + // System.out.println(" ---Tridiag transform matrix ---"); + // symm.print(System.out); + // System.out.println(); + // System.out.println(" --- D vector ---"); + // symm.printD(System.out); + // System.out.println(); + // System.out.println(" --- E vector ---"); + // symm.printE(System.out); + // System.out.println(); + // Now produce the diagonalization matrix + // tstart = System.currentTimeMillis(); + symm.tqli(); + // tend = System.currentTimeMillis(); + + // System.out.println("Time take for tqli = " + (tend-tstart) + " ms"); + // System.out.println(" --- New diagonalization matrix ---"); + // symm.print(System.out); + // System.out.println(); + // System.out.println(" --- D vector ---"); + // symm.printD(System.out); + // System.out.println(); + // System.out.println(" --- E vector ---"); + // symm.printE(System.out); + // System.out.println(); + // System.out.println(" --- First eigenvector --- "); + // double[] eigenv = symm.getColumn(0); + // for (int i=0; i < eigenv.length;i++) { + // Format.print(System.out,"%15.4f",eigenv[i]); + // } + // System.out.println(); + // double[] neigenv = origsymm.vectorPostMultiply(eigenv); + // for (int i=0; i < neigenv.length;i++) { + // Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]); + // } + // System.out.println(); + } +} diff --git a/test/jalview/util/FormatTest.java b/test/jalview/util/FormatTest.java index 1404f0b..999e456 100644 --- a/test/jalview/util/FormatTest.java +++ b/test/jalview/util/FormatTest.java @@ -21,6 +21,7 @@ package jalview.util; import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; import jalview.gui.JvOptionPane; @@ -96,4 +97,69 @@ public class FormatTest assertEquals(Format.repeat('b', 0), ""); assertEquals(Format.repeat('c', -1), ""); } + + @Test(groups = "Functional") + public void testFormat_scientific() + { + Format f = new Format("%3.4e"); + double d = 1d; + assertEquals(f.form(d), "1.0000e+000"); + assertEquals(String.format("%3.4e", d), "1.0000e+00"); + + d = 12345678.12345678d; + assertEquals(f.form(d), "1.2346e+007"); + assertEquals(String.format("%3.4e", d), "1.2346e+07"); + } + + /** + * Test that fails (in 2.10.1) with timeout as there is an infinite loop in + * Format.exp_format() + */ + @Test(groups = "Functional", timeOut = 500) + public void testFormat_scientific_overflow() + { + Format f = new Format("%3.4e"); + double d = 1.12E-310; + /* + * problem: exp_format() scales up 'd' to the range 1-10 + * while computing a scaling factor, but this factor acquires + * the value Double.POSITIVE_INFINITY instead of 1.0E+309 + * the value to be formatted is multipled by factor and becomes Infinity + * resulting in an infinite loop in the recursive call to exp_format() + */ + assertEquals(f.form(d), "1.1200e-310"); + } + + /** + * This test shows that Format.form() is faster for this case than + * String.format() + */ + @Test(groups = "Timing") + public void testFormat_scientificTiming() + { + Format f = new Format("%3.4e"); + double d = 12345678.12345678d; + + int iterations = 1000; + long start = System.currentTimeMillis(); + for (int i = 0; i < iterations; i++) + { + f.form(d); + } + long stop = System.currentTimeMillis(); + long elapsed1 = stop - start; + System.out.println(iterations + " x Format.form took " + elapsed1 + + "ms"); + + start = System.currentTimeMillis(); + for (int i = 0; i < iterations; i++) + { + String.format("%3.4e", d); + } + stop = System.currentTimeMillis(); + long elapsed2 = stop - start; + System.out.println(iterations + " x String.format took " + elapsed2 + + "ms"); + assertTrue(elapsed2 > elapsed1); + } } diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java index 3573f50..2d317e4 100644 --- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java +++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java @@ -138,7 +138,7 @@ public class DisorderAnnotExportImport { try { - String aligfileout = FileFormat.Pfam.getAlignmentFile().print( + String aligfileout = FileFormat.Pfam.getWriter(al).print( al.getSequencesArray(), true); String anfileout = new AnnotationFile() .printAnnotationsForAlignment(al); diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java index b8fe0a3..d5b6ed1 100644 --- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java +++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java @@ -188,7 +188,7 @@ public class JpredJabaStructExportImport try { // what format would be appropriate for RNAalifold annotations? - String aligfileout = FileFormat.Pfam.getAlignmentFile().print( + String aligfileout = FileFormat.Pfam.getWriter(null).print( al.getSequencesArray(), true); String anfileout = new AnnotationFile() diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 06c803f..f1430f6 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -201,7 +201,7 @@ public class RNAStructExportImport try { // what format would be appropriate for RNAalifold annotations? - String aligfileout = FileFormat.Pfam.getAlignmentFile().print( + String aligfileout = FileFormat.Pfam.getWriter(null).print( al.getSequencesArray(), true); String anfileout = new AnnotationFile() diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 45c5412..d805e47 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,6 +20,9 @@ */ package jalview.ws.sifts; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + import jalview.api.DBRefEntryI; import jalview.bin.Cache; import jalview.datamodel.DBRefEntry; @@ -178,7 +181,7 @@ public class SiftsClientTest } @BeforeTest(alwaysRun = true) - public void setUpSiftsClient() throws SiftsException + public void setUpSiftsClient() throws SiftsException, IOException { // read test props before manipulating config Cache.loadProperties("test/jalview/io/testProps.jvprops"); @@ -191,15 +194,9 @@ public class SiftsClientTest SiftsSettings.setCacheThresholdInDays("2"); SiftsSettings.setFailSafePIDThreshold("70"); PDBfile pdbFile; - try - { - pdbFile = new PDBfile(false, false, false, "test/jalview/io/" - + testPDBId + ".pdb", DataSourceType.FILE); - siftsClient = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + pdbFile = new PDBfile(false, false, false, "test/jalview/io/" + + testPDBId + ".pdb", DataSourceType.FILE); + siftsClient = new SiftsClient(pdbFile); } @AfterTest(alwaysRun = true) @@ -208,44 +205,56 @@ public class SiftsClientTest siftsClient = null; } - @Test(groups = { "Functional" }) - public void getSIFTsFileTest() throws SiftsException + @Test(groups = { "Network" }) + public void getSIFTsFileTest() throws SiftsException, IOException { File siftsFile; - try - { - siftsFile = SiftsClient.downloadSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - // test for SIFTs file caching - SiftsSettings.setCacheThresholdInDays("0"); - siftsFile = SiftsClient.getSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - SiftsSettings.setCacheThresholdInDays("2"); - } catch (IOException e) + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t1 = siftsFile.lastModified(); + + // re-read file should be returned from cache + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t2 = siftsFile.lastModified(); + assertEquals(t1, t2); + + /* + * force fetch by having 0 expiry of cache + * also wait one second, because file timestamp does not + * give millisecond resolution :-( + */ + synchronized (this) { - e.printStackTrace(); + try + { + wait(1000); + } catch (InterruptedException e) + { + } } + SiftsSettings.setCacheThresholdInDays("0"); + siftsFile = SiftsClient.getSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t3 = siftsFile.lastModified(); + assertTrue(t3 > t2, "file timestamp unchanged at " + t3); + + SiftsSettings.setCacheThresholdInDays("2"); } - @Test(groups = { "Functional" }) - public void downloadSiftsFileTest() throws SiftsException + @Test(groups = { "Network" }) + public void downloadSiftsFileTest() throws SiftsException, IOException { // Assert that file isn't yet downloaded - if already downloaded, assert it // is deleted Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId)); File siftsFile; - try - { - siftsFile = SiftsClient.downloadSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - SiftsClient.downloadSiftsFile(testPDBId); - } catch (IOException e) - { - e.printStackTrace(); - } + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + SiftsClient.downloadSiftsFile(testPDBId); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getAllMappingAccessionTest() { Assert.assertNotNull(siftsClient); @@ -253,7 +262,7 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getGreedyMappingTest() { Assert.assertNotNull(siftsClient); @@ -279,7 +288,7 @@ public class SiftsClientTest } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void getAtomIndexTest() { ArrayList atoms = new ArrayList(); @@ -294,21 +303,21 @@ public class SiftsClientTest } @Test( - groups = { "Functional" }, + groups = { "Network" }, expectedExceptions = IllegalArgumentException.class) private void getAtomIndexNullTest() { siftsClient.getAtomIndex(1, null); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void padWithGapsTest() { } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest1() throws IllegalArgumentException, SiftsException @@ -317,7 +326,7 @@ public class SiftsClientTest } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest2() throws IllegalArgumentException, SiftsException @@ -325,40 +334,29 @@ public class SiftsClientTest siftsClient.populateAtomPositions("A", null); } - @Test(groups = { "Functional" }) - public void getValidSourceDBRefTest() + @Test(groups = { "Network" }) + public void getValidSourceDBRefTest() throws SiftsException { - try - { - DBRefEntryI actualValidSrcDBRef = siftsClient - .getValidSourceDBRef(testSeq); - DBRefEntryI expectedDBRef = new DBRefEntry(); - expectedDBRef.setSource(DBRefSource.UNIPROT); - expectedDBRef.setAccessionId("P00221"); - expectedDBRef.setVersion(""); - Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); - } catch (Exception e) - { - } + DBRefEntryI actualValidSrcDBRef = siftsClient + .getValidSourceDBRef(testSeq); + DBRefEntryI expectedDBRef = new DBRefEntry(); + expectedDBRef.setSource(DBRefSource.UNIPROT); + expectedDBRef.setAccessionId("P00221"); + expectedDBRef.setVersion(""); + Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) public void getValidSourceDBRefExceptionTest() throws SiftsException { SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); - try - { - siftsClient.getValidSourceDBRef(invalidTestSeq); - } catch (SiftsException e) - { - throw new SiftsException(e.getMessage()); - } + siftsClient.getValidSourceDBRef(invalidTestSeq); } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) public void getValidSourceDBRefExceptionXTest() throws SiftsException { @@ -366,17 +364,10 @@ public class SiftsClientTest DBRefEntry invalidDBRef = new DBRefEntry(); invalidDBRef.setAccessionId("BLAR"); invalidTestSeq.addDBRef(invalidDBRef); - try - { - siftsClient.getValidSourceDBRef(invalidTestSeq); - } catch (SiftsException e) - { - throw new SiftsException(e.getMessage()); - } - + siftsClient.getValidSourceDBRef(invalidTestSeq); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void isValidDBRefEntryTest() { DBRefEntryI validDBRef = new DBRefEntry(); @@ -386,38 +377,32 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef)); } - @Test(groups = { "Functional" }) - public void getSiftsStructureMappingTest() + @Test(groups = { "Network" }) + public void getSiftsStructureMappingTest() throws SiftsException { - try - { - Assert.assertTrue(SiftsSettings.isMapWithSifts()); - StructureMapping strucMapping = siftsClient.getSiftsStructureMapping( - testSeq, testPDBId, "A"); - String expectedMappingOutput = "\nSequence â· Structure mapping details\n" - + "Method: SIFTS\n\n" - + "P00221 : 51 - 147 Maps to \n" - + "1A70|A : 1 - 97\n\n" - + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n" - + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n" - + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n" - - + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n" - + " |||||||||||||||||||||||||| |||||\n" - + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" + - - "Length of alignment = 97\n" + "Percentage ID = 98.97\n"; - - Assert.assertEquals(strucMapping.getMappingDetailsOutput(), - expectedMappingOutput); - Assert.assertEquals(strucMapping.getMapping(), expectedMapping); - } catch (SiftsException e) - { - e.printStackTrace(); - } + Assert.assertTrue(SiftsSettings.isMapWithSifts()); + StructureMapping strucMapping = siftsClient.getSiftsStructureMapping( + testSeq, testPDBId, "A"); + String expectedMappingOutput = "\nSequence â· Structure mapping details\n" + + "Method: SIFTS\n\n" + + "P00221 : 51 - 147 Maps to \n" + + "1A70|A : 1 - 97\n\n" + + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n" + + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n" + + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n" + + + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n" + + " |||||||||||||||||||||||||| |||||\n" + + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" + + + "Length of alignment = 97\n" + "Percentage ID = 98.97\n"; + + Assert.assertEquals(strucMapping.getMappingDetailsOutput(), + expectedMappingOutput); + Assert.assertEquals(strucMapping.getMapping(), expectedMapping); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getEntityCountTest() { int actualEntityCount = siftsClient.getEntityCount(); @@ -425,7 +410,7 @@ public class SiftsClientTest Assert.assertEquals(actualEntityCount, 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbAccessionIdTest() { String actualDbAccId = siftsClient.getDbAccessionId(); @@ -433,7 +418,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbAccId, "1a70"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbCoordSysTest() { String actualDbCoordSys = siftsClient.getDbCoordSys(); @@ -441,7 +426,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbCoordSys, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbSourceTest() { String actualDbSource = siftsClient.getDbSource(); @@ -449,7 +434,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbSource, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbVersionTest() { String actualDbVersion = siftsClient.getDbVersion(); @@ -457,20 +442,15 @@ public class SiftsClientTest Assert.assertEquals(actualDbVersion, "2.0"); } - @Test(groups = { "Functional" }) - public void getEntityByMostOptimalMatchedIdTest1() + @Test(groups = { "Network" }) + public void getEntityByMostOptimalMatchedIdTest1() throws IOException, + SiftsException { SiftsClient siftsClientX = null; PDBfile pdbFile; - try - { - pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" - + ".pdb", DataSourceType.FILE); - siftsClientX = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" + + ".pdb", DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A"); Assert.assertEquals(entityA.getEntityId(), "A"); Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B"); @@ -482,23 +462,18 @@ public class SiftsClientTest } - @Test(groups = { "Functional" }) - public void getEntityByMostOptimalMatchedIdTest2() + @Test(groups = { "Network" }) + public void getEntityByMostOptimalMatchedIdTest2() throws IOException, + SiftsException { // This test is for a SIFTS file in which entity A should map to chain P for // the given PDB Id. All the other chains shouldn't be mapped as there are // no SIFTS entity records for them. SiftsClient siftsClientX = null; PDBfile pdbFile; - try - { - pdbFile = new PDBfile(false, false, false, - "test/jalview/io/3ucu.cif", DataSourceType.FILE); - siftsClientX = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif", + DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P"); Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A"); Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");