g5;Date Of;5
g6;Miscellenous;6
#
+_data_column.primary_key;pdb_id
+_data_column.default_response_page_size;100
+#
_data_column.name
_data_column.code
_data_column.group_id
+_data_column.data_type
_data_column.min_col_width
_data_column.max_col_width
_data_column.preferred_col_width
-_data_column.is_primary_key
_data_column.is_shown_by_default
_data_column.is_searchable
-PDB Id;pdb_id;g2;40;60;45;true;true;true
-Title;title;g6;300;1500;400;false;true;false
-Molecule;molecule_name;g3;50;400;95;false;false;true
-Molecule Type;molecule_type;g3;50;400;95;false;false;true
-Sequence;molecule_sequence;g6;50;400;95;false;false;false
-PFAM Accession;pfam_accession;g2;50;400;95;false;false;true
-PFAM Name;pfam_name;g3;50;400;95;false;false;true
-InterPro Name;interpro_name;g3;50;400;95;false;false;false
-InterPro Accession;interpro_accession;g2;50;400;95;false;false;false
-UniProt Id;uniprot_id;g2;50;400;95;false;false;true
-UniProt Accession;uniprot_accession;g2;50;400;95;false;false;false
-UniProt Coverage;uniprot_coverage;g6;50;400;95;false;false;false
-Uniprot Features;uniprot_features;g6;50;400;95;false;false;false
-R Factor;r_factor;g1;50;150;85;false;false;false
-Resolution;resolution;g1;50;150;85;false;true;false
-Data Quality;data_quality;g1;50;150;85;false;false;false
-Overall Quality;overall_quality;g1;50;150;85;false;false;false
-Number of Polymers;number_of_polymers;g6;50;400;95;false;false;false
-Number of Protein Chains;number_of_protein_chains;g6;50;400;95;false;false;false
-Number of Bound Molecule;number_of_bound_molecules;g6;50;400;95;false;false;false
-Number of Polymer Residue;number_of_polymer_residues;g6;50;400;95;false;false;false
-GENUS;genus;g3;50;400;95;false;false;true
-Gene Name;gene_name;g3;50;400;95;false;false;true
-Experimental Method;experimental_method;g4;50;400;95;false;false;false
-GO Id;go_id;g2;50;400;95;false;false;false
-Assembly Id;assembly_id;g2;50;400;95;false;false;false
-Assembly Form;assembly_form;g6;50;400;95;false;false;false
-Assembly Type;assembly_type;g6;50;400;95;false;false;false
-Space Group;spacegroup;g6;50;400;95;false;false;false
-Cath Code;cath_code;g2;50;400;95;false;false;false
-Tax Id;tax_id;g2;50;400;95;false;false;false
-Tax Query;tax_query;g2;50;400;95;false;false;false
-Interacting Entity Id;interacting_entity_id;g2;50;400;95;false;false;false
-Interacting Molecules;interacting_molecules;g6;50;400;95;false;false;false
-Pubmed Id;pubmed_id;g2;50;400;95;false;false;false
-Status;status;g6;50;400;95;false;false;false
-Model Quality;model_quality;g1;50;150;85;false;false;false
-Pivot Resolution;pivot_resolution;g1;50;150;85;false;false;false
-Data reduction software;data_reduction_software;g4;50;400;95;false;false;false
-Max observed residues;max_observed_residues;g6;50;400;95;false;false;false
-Organism scientific name;organism_scientific_name;g3;50;400;95;false;false;false
-Super kingdom;superkingdom;g3;50;400;95;false;false;false
-Rank;rank;g3;50;400;95;false;false;false
-Crystallisation Ph;crystallisation_ph;g6;50;400;95;false;false;false
-Biological Function;biological_function;g6;50;400;95;false;false;false
-Biological Process;biological_process;g6;50;400;95;false;false;false
-Biological Cell Component;biological_cell_component;g6;50;400;95;false;false;false
-Compound Name;compound_name;g3;50;400;95;false;false;false
-Compound Id;compound_id;g2;50;400;95;false;false;false
-Compound Weight;compound_weight;g6;50;400;95;false;false;false
-Compound Systematic Name;compound_systematic_name;g3;50;400;95;false;false;false
-Interacting Ligands;interacting_ligands;g6;50;400;95;false;false;false
-Journal;journal;g6;50;400;95;false;false;false
-All Authors;all_authors;g6;50;400;95;false;false;false
-Experiment Data Available;experiment_data_available;g6;50;400;95;false;false;false
-Diffraction Protocol;diffraction_protocol;g4;50;400;95;false;false;false
-Refinement Software;refinement_software;g4;50;400;95;false;false;false
-Structure Determination Method;structure_determination_method;g4;50;400;95;false;false;false
-Synchrotron Site;synchrotron_site;g6;50;400;95;false;false;false
-Sample Preparation Method;sample_preparation_method;g4;50;400;95;false;false;false
-Entry Authors;entry_authors;g6;50;400;95;false;false;false
-Citation Title;citation_title;g6;50;400;95;false;false;false
-Structure Solution Software;structure_solution_software;g4;50;400;95;false;false;false
-Entry Entity;entry_entity;g6;50;400;95;false;false;false
-R Free;r_free;g1;50;150;85;false;false;false
-Number of Polymer Entities;number_of_polymer_entities;g6;50;400;95;false;false;false
-Number of Bound Entities;number_of_bound_entities;g6;50;400;95;false;false;false
-Crystallisation Reservoir;crystallisation_reservoir;g6;50;400;95;false;false;false
-Data Scalling Software;data_scaling_software;g4;50;400;95 ;false;false;false
-Detector;detector;g6;50;400;95;false;false;false
-Detector Type;detector_type;g6;50;400;95;false;false;false
-Modified Residue Flag;modified_residue_flag;g6;50;400;95;false;false;false
-Number of Copies;number_of_copies;g6;50;400;95;false;false;false
-Struc Asym Id;struct_asym_id;g2;50;400;95;false;false;false
-Homologus PDB Entity Id;homologus_pdb_entity_id;g2;50;400;95;false;false;false
-Molecule Synonym;molecule_synonym;g6;50;400;95;false;false;false
-Deposition Site;deposition_site;g6;50;400;95;false;false;false
-Synchrotron Beamline;synchrotron_beamline;g6;50;400;95;false;false;false
-Entity Id; entity_id;g2;50;400;95;false;false;false
-Beam Source Name;beam_source_name;g3;50;400;95;false;false;false
-Processing Site;processing_site;g6;50;400;95;false;false;false
-Entity Weight;entity_weight;g6;50;400;95;false;false;false
-Version;_version_;g6;50;400;95;false;false;false
-ALL;text;g6;50;400;95;false;false;true
+PDB Id;pdb_id;String;g2;40;60;45;true;true
+Title;title;String;g6;300;1500;400;true;false
+Molecule;molecule_name;String;g3;50;400;95;false;true
+Molecule Type;molecule_type;String;g3;50;400;95;false;true
+Sequence;molecule_sequence;String;g6;50;400;95;false;false
+PFAM Accession;pfam_accession;String;g2;50;400;95;false;true
+PFAM Name;pfam_name;String;g3;50;400;95;false;true
+InterPro Name;interpro_name;String;g3;50;400;95;false;false
+InterPro Accession;interpro_accession;String;g2;50;400;95;false;false
+UniProt Id;uniprot_id;String;g2;50;400;95;false;true
+UniProt Accession;uniprot_accession;String;g2;50;400;95;false;false
+UniProt Coverage;uniprot_coverage;String;g6;50;400;95;false;false
+Uniprot Features;uniprot_features;String;g6;50;400;95;false;false
+R Factor;r_factor;Double;g1;50;150;85;false;false
+Resolution;resolution;Double;g1;50;150;85;true;false
+Data Quality;data_quality;Double;g1;50;150;85;false;false
+Overall Quality;overall_quality;Double;g1;50;150;85;false;false
+Number of Polymers;number_of_polymers;int;g6;50;400;95;false;false
+Number of Protein Chains;number_of_protein_chains;int;g6;50;400;95;false;false
+Number of Bound Molecule;number_of_bound_molecules;int;g6;50;400;95;false;false
+Number of Polymer Residue;number_of_polymer_residues;int;g6;50;400;95;false;false
+GENUS;genus;String;g3;50;400;95;false;true
+Gene Name;gene_name;String;g3;50;400;95;false;true
+Experimental Method;experimental_method;String;g4;50;400;95;false;false
+GO Id;go_id;String;g2;50;400;95;false;false
+Assembly Id;assembly_id;String;g2;50;400;95;false;false
+Assembly Form;assembly_form;String;g6;50;400;95;false;false
+Assembly Type;assembly_type;String;g6;50;400;95;false;false
+Space Group;spacegroup;String;g6;50;400;95;false;false
+Cath Code;cath_code;String;g2;50;400;95;false;false
+Tax Id;tax_id;String;g2;50;400;95;false;false
+Tax Query;tax_query;String;g2;50;400;95;false;false
+Interacting Entity Id;interacting_entity_id;String;g2;50;400;95;false;false
+Interacting Molecules;interacting_molecules;String;g6;50;400;95;false;false
+Pubmed Id;pubmed_id;int;g2;50;400;95;false;false
+Status;status;String;g6;50;400;95;false;false
+Model Quality;model_quality;Double;g1;50;150;85;false;false
+Pivot Resolution;pivot_resolution;Double;g1;50;150;85;false;false
+Data reduction software;data_reduction_software;String;g4;50;400;95;false;false
+Max observed residues;max_observed_residues;String;g6;50;400;95;false;false
+Organism scientific name;organism_scientific_name;String;g3;50;400;95;false;false
+Super kingdom;superkingdom;String;g3;50;400;95;false;false
+Rank;rank;String;g3;50;400;95;false;false
+Crystallisation Ph;crystallisation_ph;String;g6;50;400;95;false;false
+Biological Function;biological_function;String;g6;50;400;95;false;false
+Biological Process;biological_process;String;g6;50;400;95;false;false
+Biological Cell Component;biological_cell_component;String;g6;50;400;95;false;false
+Compound Name;compound_name;String;g3;50;400;95;false;false
+Compound Id;compound_id;String;g2;50;400;95;false;false
+Compound Weight;compound_weight;String;g6;50;400;95;false;false
+Compound Systematic Name;compound_systematic_name;String;g3;50;400;95;false;false
+Interacting Ligands;interacting_ligands;String;g6;50;400;95;false;false
+Journal;journal;String;g6;50;400;95;false;false
+All Authors;all_authors;String;g6;50;400;95;false;false
+Experiment Data Available;experiment_data_available;String;g6;50;400;95;false;false
+Diffraction Protocol;diffraction_protocol;String;g4;50;400;95;false;false
+Refinement Software;refinement_software;String;g4;50;400;95;false;false
+Structure Determination Method;structure_determination_method;String;g4;50;400;95;false;false
+Synchrotron Site;synchrotron_site;String;g6;50;400;95;false;false
+Sample Preparation Method;sample_preparation_method;String;g4;50;400;95;false;false
+Entry Authors;entry_authors;String;g6;50;400;95;false;false
+Citation Title;citation_title;String;g6;50;400;95;false;false
+Structure Solution Software;structure_solution_software;String;g4;50;400;95;false;false
+Entry Entity;entry_entity;String;g6;50;400;95;false;false
+R Free;r_free;Double;g1;50;150;85;false;false
+Number of Polymer Entities;number_of_polymer_entities;int;g6;50;400;95;false;false
+Number of Bound Entities;number_of_bound_entities;int;g6;50;400;95;false;false
+Crystallisation Reservoir;crystallisation_reservoir;String;g6;50;400;95;false;false
+Data Scalling Software;data_scaling_software;String;g4;50;400;95;false;false
+Detector;detector;String;g6;50;400;95;false;false
+Detector Type;detector_type;String;g6;50;400;95;false;false
+Modified Residue Flag;modified_residue_flag;String;g6;50;400;95;false;false
+Number of Copies;number_of_copies;int;g6;50;400;95;false;false
+Struc Asym Id;struct_asym_id;String;g2;50;400;95;false;false
+Homologus PDB Entity Id;homologus_pdb_entity_id;String;g2;50;400;95;false;false
+Molecule Synonym;molecule_synonym;String;g6;50;400;95;false;false
+Deposition Site;deposition_site;String;g6;50;400;95;false;false
+Synchrotron Beamline;synchrotron_beamline;String;g6;50;400;95;false;false
+Entity Id; entity_id;String;g2;50;400;95;false;false
+Beam Source Name;beam_source_name;String;g3;50;400;95;false;false
+Processing Site;processing_site;String;g6;50;400;95;false;false
+Entity Weight;entity_weight;Double;g6;50;400;95;false;false
+Version;_version_;String;g6;50;400;95;false;false
+ALL;text;String;g6;50;400;95;false;true
#
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.api;
+/**
+ * This interface provides a model for the summary data;
+ *
+ * @author tcnofoegbu
+ *
+ */
public interface FTSData
{
+
+ /**
+ * Return an array of Objects representing the retrieved FTS data
+ *
+ * @return
+ */
public Object[] getSummaryData();
+ /**
+ * The primary key object for the retrieved FTS data
+ *
+ * @return
+ */
public Object getPrimaryKey();
}
+++ /dev/null
-package jalview.fts.api;
-
-public interface FTSDataColumnGroupI
-{
- public String getID();
-
- public String getName();
-
- public int getSortOrder();
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.api;
+/**
+ * This interface provides a model for the dynamic data column configuration
+ *
+ * @author tcnofoegbu
+ *
+ */
public interface FTSDataColumnI
{
+ /**
+ * Returns the name of the data column
+ *
+ * @return the data column's name
+ */
public String getName();
+ /**
+ * Returns the code of the data column
+ *
+ * @return the data column's code
+ */
public String getCode();
+ /**
+ * Returns the minimum width of the data column
+ *
+ * @return the data column's minimum width
+ */
public int getMinWidth();
+ /**
+ * Returns the maximum width of the data column
+ *
+ * @return the data column's maximum width
+ */
public int getMaxWidth();
+ /**
+ * Returns the preferred width of the data column
+ *
+ * @return the data column's preferred width
+ */
public int getPreferredWidth();
+ /**
+ * Determines if the data column is the primary key column
+ *
+ * @return true if data column is the primary key column, otherwise false
+ */
public boolean isPrimaryKeyColumn();
+ /**
+ * Checks if the data column field can be used to perform a search query
+ *
+ * @return true means the data column is searchable
+ */
public boolean isSearchable();
+ /**
+ * Checks if the data column is displayed by default
+ *
+ * @return true means the data column is shown by default
+ */
public boolean isVisibleByDefault();
+ /**
+ * Returns the data column's data type class
+ *
+ * @return the Class for the data column's data type
+ */
+ public Class getDataColumnClass();
+
+ /**
+ * Returns the data colum's FTS data column group
+ *
+ * @return the FTSDataColumnGroupI for the column
+ */
public FTSDataColumnGroupI getGroup();
+
+ /**
+ * This interface provides a model for the dynamic data column group
+ *
+ */
+ public interface FTSDataColumnGroupI
+ {
+ /**
+ * Returns the Id of the data column's group
+ *
+ * @return the data column's group Id
+ */
+ public String getID();
+
+ /**
+ * Returns the name of the group
+ *
+ * @return the group's name
+ */
+ public String getName();
+
+ /**
+ * Returns the sort order of the group
+ *
+ * @return the group's sort order
+ */
+ public int getSortOrder();
+ }
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.api;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import java.util.Collection;
+/**
+ * Methods for FTS Rest client.
+ *
+ * @author tcnofoegbu
+ */
public interface FTSRestClientI
{
- public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
+ /**
+ * Execute a given FTS request, process the response and return it as an
+ * FTSRestResponse object
+ *
+ * @param ftsRestRequest
+ * the FTS request to execute
+ * @return FTSRestResponse - the response after executing an FTS request
+ * @throws Exception
+ */
+ public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
throws Exception;
- public String getColumnDataConfigFile();
+ /**
+ * Return the resource file path for the data columns configuration file
+ *
+ * @return
+ */
+ public String getColumnDataConfigFileName();
- public FTSDataColumnGroupI getDataColumnGroupById(String id)
+ /**
+ * Fetch FTSDataColumnGroupI by the group's Id
+ *
+ * @param groupId
+ * @return FTSDataColumnGroupI
+ * @throws Exception
+ */
+ public FTSDataColumnGroupI getDataColumnGroupById(String groupId)
throws Exception;
+ /**
+ * Fetch FTSDataColumnI by name or code
+ *
+ * @param nameOrCode
+ * @return FTSDataColumnI
+ * @throws Exception
+ */
public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
throws Exception;
+
+ /**
+ * Convert collection of FTSDataColumnI objects to a comma delimited string of
+ * the 'code' values
+ *
+ * @param wantedFields
+ * the collection of FTSDataColumnI to process
+ * @return the generated comma delimited string from the supplied
+ * FTSDataColumnI collection
+ */
+ public String getDataColumnsFieldsAsCommaDelimitedString(
+ Collection<FTSDataColumnI> wantedFields);
+
+
+ /**
+ * Fetch index of the primary key column for the dynamic table
+ *
+ * @param wantedFields
+ * the available table columns
+ * @param hasRefSeq
+ * true if the data columns has an additional column for reference
+ * sequence
+ * @return index of the primary key column
+ * @throws Exception
+ */
public int getPrimaryKeyColumIndex(
Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq)
throws Exception;
+ /**
+ * Fetch the primary key data column object
+ *
+ * @return the FTSDataColumnI object for the primary key column
+ */
public FTSDataColumnI getPrimaryKeyColumn();
+ /**
+ * Returns list of FTSDataColumnI objects to be displayed by default
+ *
+ * @return list of columns to display by default
+ */
public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns();
+ /**
+ * Return list of FTSDataColumnI objects that can be used to perform a search
+ * query
+ *
+ * @return list of searchable FTSDataColumnI object
+ */
public Collection<FTSDataColumnI> getSearchableDataColumns();
+ /**
+ * Return list of all available FTSDataColumnI object
+ *
+ * @return list of all FTSColumnI objcet
+ */
public Collection<FTSDataColumnI> getAllFTSDataColumns();
+
+ /**
+ * Return the default response page limit
+ *
+ * @return the default response page size
+ */
+ public int getDefaultResponsePageSize();
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.fts.api;
+
+import javax.swing.JTable;
+
+/**
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface GFTSPanelI
+{
+
+ /**
+ * Action performed when a text is entered in the search field.
+ */
+ public void searchAction();
+
+ /**
+ * Action performed when search results are selected and the 'ok' button is
+ * pressed.
+ */
+ public void okAction();
+
+ /**
+ * Return the entered text
+ *
+ * @return the entered text
+ */
+ public String getTypedText();
+
+ /**
+ * The JTable for presenting the query result
+ *
+ * @return JTable
+ */
+ public JTable getResultTable();
+
+ /**
+ * Return the title to display on the search interface main panel
+ *
+ * @return String - the title
+ */
+ public String getFTSFrameTitle();
+
+ /**
+ * Return a singleton instance of FTSRestClientI
+ *
+ * @return FTSRestClientI
+ */
+ public FTSRestClientI getFTSRestClient();
+
+ /**
+ * Set error message when one occurs
+ *
+ * @param message
+ * the error message to set
+ */
+ public void setErrorMessage(String message);
+
+ /**
+ * Updates the title displayed on the search interface's main panel
+ *
+ * @param newTitle
+ */
+ public void updateSearchFrameTitle(String newTitle);
+
+ /**
+ * Controls the progress spinner, set to 'true' while search operation is in
+ * progress and 'false' after it completes
+ *
+ * @param isSearchInProgress
+ */
+ public void setSearchInProgress(Boolean isSearchInProgress);
+}
*/
package jalview.fts.core;
-import jalview.fts.api.FTSDataColumnGroupI;
import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
import java.util.ArrayList;
private HashMap<String, FTSDataColumnI> map = new HashMap<String, FTSDataColumnI>();
- private static Collection<FTSDataColumnI> structSummaryColumns = new LinkedHashSet<FTSDataColumnI>();
+ private Collection<FTSDataColumnI> structSummaryColumns = new LinkedHashSet<FTSDataColumnI>();
private Collection<FTSDataColumnI> allFTSDataColumns = new LinkedHashSet<FTSDataColumnI>();
}
- public static Collection<FTSDataColumnI> getStructureSummaryFields()
+ public Collection<FTSDataColumnI> getStructureSummaryFields()
{
return structSummaryColumns;
}
- public static void setStructureSummaryFields(
- Collection<FTSDataColumnI> structureSummaryFields)
- {
- FTSDataColumnPreferences.structSummaryColumns = structureSummaryFields;
- }
-
class FTSDataColumnPrefsTableModel extends AbstractTableModel
{
package jalview.fts.core;
-import jalview.fts.api.FTSDataColumnGroupI;
import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
import java.io.BufferedReader;
import java.util.Collection;
import java.util.Objects;
+/**
+ * Base class providing implementation for common methods defined in
+ * FTSRestClientI
+ *
+ * @author tcnofoegbu
+ *
+ * @note implementations MUST be accessed as a singleton.
+ */
public abstract class FTSRestClient implements FTSRestClientI
{
protected Collection<FTSDataColumnI> dataColumns = new ArrayList<FTSDataColumnI>();
protected FTSDataColumnI primaryKeyColumn;
+ private String primaryKeyColumnCode = null;
+
+ private int defaultResponsePageSize = 100;
+
protected FTSRestClient()
{
}
- public void parseDataColumnsFile()
+ public void parseDataColumnsConfigFile()
{
- String fileName = getColumnDataConfigFile();
+ String fileName = getColumnDataConfigFileName();
try (BufferedReader br = new BufferedReader(new FileReader(fileName)))
{
String line;
while ((line = br.readLine()) != null)
{
final String[] lineData = line.split(";");
- if (lineData.length == 3)
+ try
{
- dataColumnGroups.add(new FTSDataColumnGroupI()
+ if (lineData.length == 2)
{
- @Override
- public String getID()
+ if (lineData[0].equalsIgnoreCase("_data_column.primary_key"))
{
- return lineData[0];
+ primaryKeyColumnCode = lineData[1];
}
-
- @Override
- public String getName()
+ if (lineData[0]
+ .equalsIgnoreCase("_data_column.default_response_page_size"))
{
- return lineData[1];
+ defaultResponsePageSize = Integer.valueOf(lineData[1]);
}
-
- @Override
- public int getSortOrder()
+ }
+ else if (lineData.length == 3)
+ {
+ dataColumnGroups.add(new FTSDataColumnGroupI()
{
- return Integer.valueOf(lineData[2]);
- }
+ @Override
+ public String getID()
+ {
+ return lineData[0];
+ }
- @Override
- public String toString()
- {
- return lineData[1];
- }
+ @Override
+ public String getName()
+ {
+ return lineData[1];
+ }
- @Override
- public int hashCode()
- {
- return Objects.hash(this.getID(), this.getName(),
- this.getSortOrder());
- }
+ @Override
+ public int getSortOrder()
+ {
+ return Integer.valueOf(lineData[2]);
+ }
- @Override
- public boolean equals(Object otherObject)
- {
- FTSDataColumnGroupI that = (FTSDataColumnGroupI) otherObject;
- return this.getID().equals(that.getID())
- && this.getName().equals(that.getName())
- && this.getSortOrder() == that.getSortOrder();
- }
- });
- }
- else if (lineData.length > 6)
- {
- FTSDataColumnI dataCol = new FTSDataColumnI()
+ @Override
+ public String toString()
+ {
+ return lineData[1];
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.getID(), this.getName(),
+ this.getSortOrder());
+ }
+
+ @Override
+ public boolean equals(Object otherObject)
+ {
+ FTSDataColumnGroupI that = (FTSDataColumnGroupI) otherObject;
+ return this.getID().equals(that.getID())
+ && this.getName().equals(that.getName())
+ && this.getSortOrder() == that.getSortOrder();
+ }
+ });
+ }
+ else if (lineData.length > 6)
{
- @Override
- public String toString()
+ FTSDataColumnI dataCol = new FTSDataColumnI()
{
- return lineData[0];
- }
+ @Override
+ public String toString()
+ {
+ return lineData[0];
+ }
- @Override
- public String getName()
- {
- return lineData[0];
- }
+ @Override
+ public String getName()
+ {
+ return lineData[0];
+ }
- @Override
- public String getCode()
- {
- return lineData[1];
- }
+ @Override
+ public String getCode()
+ {
+ return lineData[1];
+ }
- @Override
- public FTSDataColumnGroupI getGroup()
- {
- FTSDataColumnGroupI group = null;
- try
+ @Override
+ public Class<?> getDataColumnClass()
{
- group = getDataColumnGroupById(lineData[2]);
- } catch (Exception e)
+ String classString = lineData[2];
+ classString = classString.toUpperCase();
+ switch (classString)
+ {
+ case "INT":
+ case "INTEGER":
+ return Integer.class;
+ case "DOUBLE":
+ return Double.class;
+ case "STRING":
+ default:
+ return String.class;
+ }
+ }
+
+ @Override
+ public FTSDataColumnGroupI getGroup()
{
- e.printStackTrace();
+ FTSDataColumnGroupI group = null;
+ try
+ {
+ group = getDataColumnGroupById(lineData[3]);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return group;
}
- return group;
- }
- @Override
- public int getMinWidth()
- {
- return Integer.valueOf(lineData[3]);
- }
+ @Override
+ public int getMinWidth()
+ {
+ return Integer.valueOf(lineData[4]);
+ }
- @Override
- public int getMaxWidth()
- {
- return Integer.valueOf(lineData[4]);
- }
+ @Override
+ public int getMaxWidth()
+ {
+ return Integer.valueOf(lineData[5]);
+ }
- @Override
- public int getPreferredWidth()
- {
- return Integer.valueOf(lineData[5]);
- }
+ @Override
+ public int getPreferredWidth()
+ {
+ return Integer.valueOf(lineData[6]);
+ }
+ @Override
+ public boolean isPrimaryKeyColumn()
+ {
+ return getName().equalsIgnoreCase(primaryKeyColumnCode)
+ || getCode().equalsIgnoreCase(primaryKeyColumnCode);
+ }
- @Override
- public boolean isPrimaryKeyColumn()
- {
- return Boolean.valueOf(lineData[6]);
- }
+ @Override
+ public boolean isVisibleByDefault()
+ {
+ return Boolean.valueOf(lineData[7]);
+ }
- @Override
- public boolean isVisibleByDefault()
- {
- return Boolean.valueOf(lineData[7]);
- }
+ @Override
+ public boolean isSearchable()
+ {
+ return Boolean.valueOf(lineData[8]);
+ }
- @Override
- public boolean isSearchable()
- {
- return Boolean.valueOf(lineData[8]);
- }
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.getName(), this.getCode(),
+ this.getGroup());
+ }
- @Override
- public int hashCode()
+
+ @Override
+ public boolean equals(Object otherObject)
+ {
+ FTSDataColumnI that = (FTSDataColumnI) otherObject;
+ return this.getCode().equals(that.getCode())
+ && this.getName().equals(that.getName())
+ && this.getGroup().equals(that.getGroup());
+ }
+
+ };
+ dataColumns.add(dataCol);
+
+ if (dataCol.isSearchable())
{
- return Objects.hash(this.getName(), this.getCode(),
- this.getGroup());
+ searchableDataColumns.add(dataCol);
}
- @Override
- public boolean equals(Object otherObject)
+ if (dataCol.isVisibleByDefault())
{
- FTSDataColumnI that = (FTSDataColumnI) otherObject;
- return this.getCode().equals(that.getCode())
- && this.getName().equals(that.getName())
- && this.getGroup().equals(that.getGroup());
+ defaulDisplayedDataColumns.add(dataCol);
}
- };
- dataColumns.add(dataCol);
- if (dataCol.isSearchable())
- {
- searchableDataColumns.add(dataCol);
}
-
- if (dataCol.isVisibleByDefault())
+ else
{
- defaulDisplayedDataColumns.add(dataCol);
+ continue;
}
-
- }
- else
+ } catch (Exception e)
{
- continue;
+ e.printStackTrace();
}
}
} catch (IOException e)
}
}
- /**
- * Determines the column index for 'Primary key' Fields in the dynamic summary
- * table.
- *
- * @param wantedFields
- * the available table columns in no particular order
- * @return the primary key column index
- * @throws Exception
- */
@Override
public int getPrimaryKeyColumIndex(
- Collection<FTSDataColumnI> wantedFields,
- boolean hasRefSeq) throws Exception
+ Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq)
+ throws Exception
{
// If a reference sequence is attached then start counting from 1 else
return pdbFieldIndexCounter;
}
+ @Override
+ public String getDataColumnsFieldsAsCommaDelimitedString(
+ Collection<FTSDataColumnI> dataColumnFields)
+ {
+ String result = "";
+ if (dataColumnFields != null && !dataColumnFields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (FTSDataColumnI field : dataColumnFields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
/**
* Takes a collection of FTSDataColumnI and converts its 'code' values into a
- * comma delimited string.
+ * tab delimited string.
*
* @param dataColumnFields
* the collection of FTSDataColumnI to process
* @return the generated comma delimited string from the supplied
* FTSDataColumnI collection
*/
- public static String getDataColumnsFieldsAsCommaDelimitedString(
+ public String getDataColumnsFieldsAsTabDelimitedString(
Collection<FTSDataColumnI> dataColumnFields)
{
String result = "";
StringBuilder returnedFields = new StringBuilder();
for (FTSDataColumnI field : dataColumnFields)
{
- returnedFields.append(",").append(field.getCode());
+ returnedFields.append("\t").append(field.getName());
}
returnedFields.deleteCharAt(0);
result = returnedFields.toString();
{
if (dataColumns == null || dataColumns.isEmpty())
{
- parseDataColumnsFile();
+ parseDataColumnsConfigFile();
}
return dataColumns;
}
{
if (searchableDataColumns == null || searchableDataColumns.isEmpty())
{
- parseDataColumnsFile();
+ parseDataColumnsConfigFile();
}
return searchableDataColumns;
}
if (defaulDisplayedDataColumns == null
|| defaulDisplayedDataColumns.isEmpty())
{
- parseDataColumnsFile();
+ parseDataColumnsConfigFile();
}
return defaulDisplayedDataColumns;
}
}
@Override
- public FTSDataColumnI getDataColumnByNameOrCode(
- String nameOrCode) throws Exception
+ public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
+ throws Exception
{
+ if (dataColumns == null || dataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
for (FTSDataColumnI column : dataColumns)
{
if (column.getName().equalsIgnoreCase(nameOrCode)
public FTSDataColumnGroupI getDataColumnGroupById(String id)
throws Exception
{
+ if (dataColumns == null || dataColumns.isEmpty())
+ {
+ parseDataColumnsConfigFile();
+ }
for (FTSDataColumnGroupI columnGroup : dataColumnGroups)
{
if (columnGroup.getID().equalsIgnoreCase(id))
throw new Exception("Couldn't find data column group with id : " + id);
}
- protected String getFile(String fileName)
+ protected String getResourceFile(String fileName)
{
ClassLoader classLoader = getClass().getClassLoader();
- // File file = new File(classLoader.getResource(fileName).getFile());
String result = "";
try
{
}
+ @Override
+ public int getDefaultResponsePageSize()
+ {
+ return defaultResponsePageSize;
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import java.util.Collection;
/**
- * Represents the PDB request to be consumed by the PDBRestClient
+ * Represents the FTS request to be consumed by the FTSRestClient
*
* @author tcnofoegbu
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import javax.swing.table.DefaultTableModel;
/**
- * Represents the response model produced by the PDBRestClient upon successful
- * execution of a given request
+ * Represents the response model generated by the FTSRestClient upon successful
+ * execution of a given FTS request
*
* @author tcnofoegbu
*
* on the request parameters
*
* @param request
- * the PDBRestRequest object which holds useful information for
+ * the FTSRestRequest object which holds useful information for
* creating a table model
* @param summariesList
* the summary list which contains the data for populating the
{
return String.class;
}
- if (cols[columnIndex - colOffset].getGroup().getName()
- .equalsIgnoreCase("Quality Measures"))
- {
- return Double.class;
- }
- return String.class;
+ return cols[columnIndex - colOffset].getDataColumnClass();
}
};
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.fts.core;
import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.GFTSPanelI;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.JvSwingUtils;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
+import javax.swing.table.DefaultTableModel;
/**
- * GUI layout for PDB Fetch Panel
+ * This class provides the swing GUI layout for FTS Panel and implements most of
+ * the contracts defined in GFSPanelI
*
* @author tcnofoegbu
*
*/
@SuppressWarnings("serial")
-public abstract class GFTSPanel extends JPanel
+public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
protected Collection<FTSDataColumnI> wantedFields;
- protected JTable tbl_summary = new JTable()
+ private JTable tbl_summary = new JTable()
{
@Override
public String getToolTipText(MouseEvent evt)
case KeyEvent.VK_ENTER: // enter key
if (btn_ok.isEnabled())
{
- btn_ok_ActionPerformed();
+ okAction();
}
evt.consume();
break;
@Override
public void actionPerformed(ActionEvent e)
{
- btn_ok_ActionPerformed();
+ okAction();
}
});
btn_ok.addKeyListener(new KeyAdapter()
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER)
{
- btn_ok_ActionPerformed();
+ okAction();
}
}
});
}
txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
tooltipText));
- txt_search_ActionPerformed();
+ searchAction();
}
});
@Override
public void insertUpdate(DocumentEvent e)
{
- txt_search_ActionPerformed();
+ searchAction();
}
@Override
public void removeUpdate(DocumentEvent e)
{
- txt_search_ActionPerformed();
+ searchAction();
}
@Override
public void changedUpdate(DocumentEvent e)
{
- txt_search_ActionPerformed();
+ searchAction();
}
});
btn_back.setEnabled(false);
btn_cancel.setEnabled(false);
btn_ok.setEnabled(false);
- previousWantedFields = PDBFTSRestClient.getInstance()
+ previousWantedFields = getFTSRestClient()
.getAllDefaulDisplayedDataColumns()
.toArray(new Object[0]);
}
btn_cancel.setEnabled(true);
if (wantedFieldsUpdated())
{
- txt_search_ActionPerformed();
+ searchAction();
}
else
{
return true;
}
- return Arrays.equals(PDBFTSRestClient.getInstance()
+ return Arrays.equals(getFTSRestClient()
.getAllDefaulDisplayedDataColumns()
.toArray(new Object[0]), previousWantedFields) ? false
: true;
worker.start();
}
- public abstract String getFTSFrameTitle();
+ @Override
+ public String getTypedText()
+ {
+ return txt_search.getText().trim();
+ }
- public abstract FTSRestClientI getFTSRestClient();
+ @Override
+ public JTable getResultTable()
+ {
+ return tbl_summary;
+ }
- public abstract void txt_search_ActionPerformed();
+ public void reset()
+ {
+ lbl_loading.setVisible(false);
+ errorWarning.setLength(0);
+ lbl_warning.setVisible(false);
+ btn_ok.setEnabled(false);
+ mainFrame.setTitle(getFTSFrameTitle());
+ referesh();
+ tbl_summary.setModel(new DefaultTableModel());
+ tbl_summary.setVisible(false);
+ }
- public abstract void btn_ok_ActionPerformed();
+ @Override
+ public void setErrorMessage(String message)
+ {
+ errorWarning.append(message);
+ }
+
+ @Override
+ public void updateSearchFrameTitle(String title)
+ {
+ mainFrame.setTitle(title);
+ }
+
+ @Override
+ public void setSearchInProgress(Boolean isSearchInProgress)
+ {
+ lbl_loading.setVisible(isSearchInProgress);
+ }
+ public void referesh()
+ {
+ mainFrame.setTitle(getFTSFrameTitle());
+ }
}
import java.util.HashSet;
-import javax.swing.table.DefaultTableModel;
-
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
+ private static String defaultFTSFrameTitle = MessageManager
+ .getString("label.pdb_sequence_fetcher");
+
+ private String ftsFrameTitle = defaultFTSFrameTitle;
public PDBFTSPanel(SequenceFetcher seqFetcher)
{
}
- /**
- * Action performed when an input is detected on txt_search field.
- */
@Override
- public void txt_search_ActionPerformed()
+ public void searchAction()
{
new Thread()
{
@Override
public void run()
{
- lbl_loading.setVisible(false);
- errorWarning.setLength(0);
- lbl_warning.setVisible(false);
- btn_ok.setEnabled(false);
+ ftsFrameTitle = defaultFTSFrameTitle;
+ reset();
boolean allowEmptySequence = false;
- mainFrame.setTitle(getFTSFrameTitle());
- tbl_summary.setModel(new DefaultTableModel());
- tbl_summary.setVisible(false);
- if (txt_search.getText().trim().length() > 0)
+ if (getTypedText().length() > 0)
{
- lbl_loading.setVisible(true);
+ setSearchInProgress(true);
long startTime = System.currentTimeMillis();
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
.getSelectedItem()).getCode();
-
- // wantedFields = FTSDataColumnPreferences.getSearchSummaryFields();
wantedFields = PDBFTSRestClient.getInstance()
.getAllDefaulDisplayedDataColumns();
String searchTerm = decodeSearchTerm(txt_search.getText(),
request.setFieldToSearchBy("(" + searchTarget + ":");
request.setSearchTerm(searchTerm + ")");
request.setWantedFields(wantedFields);
- // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
FTSRestResponse resultList;
try
resultList = pdbRestCleint.executeRequest(request);
} catch (Exception e)
{
- // e.printStackTrace();
- errorWarning.append(e.getMessage());
+ setErrorMessage(e.getMessage());
checkForErrors();
return;
}
- if (resultList.getSearchSummary() != null)
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
{
- tbl_summary.setModel(FTSRestResponse.getTableModel(request,
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(request,
resultList.getSearchSummary()));
- FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
- tbl_summary.setVisible(true);
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields);
+ getResultTable().setVisible(true);
}
-
long endTime = System.currentTimeMillis();
int resultSetCount = resultList.getNumberOfItemsFound();
String result = (resultSetCount > 1) ? MessageManager
.getString("label.results") : MessageManager
.getString("label.result");
- mainFrame.setTitle(getFTSFrameTitle() + " - " + resultSetCount
- + " "
- + result + " (" + (endTime - startTime) + " milli secs)");
- lbl_loading.setVisible(false);
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ + resultSetCount + " " + result + " ("
+ + (endTime - startTime) + " milli secs)");
+ setSearchInProgress(false);
}
}
}.start();
}
@Override
- public void btn_ok_ActionPerformed()
+ public void okAction()
{
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
HashSet<String> selectedIdsSet = new HashSet<String>();
- int pdbIdCol = 0;
+ int primaryKeyColIndex = 0;
try
{
- pdbIdCol = getFTSRestClient().getPrimaryKeyColumIndex(wantedFields,
+ primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+ wantedFields,
false);
} catch (Exception e)
{
// TODO Auto-generated catch block
e.printStackTrace();
}
- int[] selectedRows = tbl_summary.getSelectedRows();
+ int[] selectedRows = getResultTable().getSelectedRows();
for (int summaryRow : selectedRows)
{
- String idStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ String idStr = getResultTable().getValueAt(summaryRow,
+ primaryKeyColIndex)
.toString();
String searchTerm = txt_search.getText();
selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
@Override
public String getFTSFrameTitle()
{
- return MessageManager.getString("label.pdb_sequence_fetcher");
+ return ftsFrameTitle;
}
+
}
import com.sun.jersey.api.client.config.DefaultClientConfig;
/**
- * A rest client for querying the Search endpoint of the PDB REST API
+ * A rest client for querying the Search endpoint of the PDB API
*
* @author tcnofoegbu
*
public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
- private static int DEFAULT_RESPONSE_SIZE = 200;
-
protected PDBFTSRestClient()
{
}
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest
.getWantedFields());
- int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
: pdbRestRequest.getResponseSize();
String sortParam = null;
if (pdbRestRequest.getFieldToSortBy() == null
primaryKey = fieldData;
summaryRowData[colCounter++] = primaryKey;
}
+ else if (fieldData == null || fieldData.isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
else
{
- if (field.getGroup().getName().equals("Quality Measures"))
+ try
{
- try
- {
- if (fieldData == null || fieldData.isEmpty())
- {
- summaryRowData[colCounter++] = null;
- }
- else
- {
- Double value = Double.valueOf(fieldData);
- summaryRowData[colCounter++] = value;
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- System.out.println("offending value:" + fieldData);
- summaryRowData[colCounter++] = 0.0;
- }
- }
- else
+ summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+ .valueOf(fieldData)
+ : (field.getDataColumnClass() == Double.class) ? Double
+ .valueOf(fieldData)
+ : fieldData;
+ } catch (Exception e)
{
- summaryRowData[colCounter++] = (fieldData == null || fieldData
- .isEmpty()) ? null : fieldData;
+ e.printStackTrace();
+ System.out.println("offending value:" + fieldData);
}
}
}
}
@Override
- public String getColumnDataConfigFile()
+ public String getColumnDataConfigFileName()
{
- return getFile("fts/pdb_data_columns.conf");
+ return getResourceFile("fts/pdb_data_columns.conf");
}
--- /dev/null
+package jalview.fts.service.uniprot;
+
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+
+import javax.ws.rs.core.MediaType;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
+public class UniProtRestClient extends FTSRestClient
+{
+ private static FTSRestClientI instance = null;
+
+ public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+
+ private static int DEFAULT_RESPONSE_SIZE = 200;
+
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ Client client = Client.create(clientConfig);
+
+ @SuppressWarnings("unchecked")
+ // String wantedFields =
+ // getUniProtDocFieldsAsCommaDelimitedString((Collection<UniProtDocField>)
+ // uniportRestRequest
+ // .getWantedFields());
+ int responseSize = (uniportRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : uniportRestRequest.getResponseSize();
+
+ WebResource webResource = null;
+
+ webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
+ .queryParam("format", "tab")
+ // .queryParam("columns", wantedFields)
+ .queryParam("limit", String.valueOf(responseSize))
+ .queryParam("query", "name:filaggrin");
+ // Execute the REST request
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
+ String responseString = clientResponse.getEntity(String.class);
+ String[] results = responseString.split("\n");
+ for (String result : results)
+ {
+ String[] columns = result.split("\t");
+ System.out.println("Entry : " + columns[0]);
+ System.out.println("Entry name : " + columns[1]);
+ System.out.println("Status : " + columns[2]);
+ System.out.println("Protein names : " + columns[3]);
+ System.out.println("Gene name : " + columns[4]);
+ System.out.println("Organism : " + columns[5]);
+ System.out.println("Lenght : " + columns[6]);
+ System.out.println("");
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+ return null;
+
+ // Process the response and return the result to the caller.
+ // return parsePDBJsonResponse(responseString, pdbRestRequest);
+ // System.out.println(">>>>> " + responseString);
+
+ }
+
+
+ public static FTSRestClientI getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new UniProtRestClient();
+ }
+ return instance;
+ }
+
+ @Override
+ public String getColumnDataConfigFile()
+ {
+ return "fts/uniprot_data_columns.conf";
+ }
+
+}
--- /dev/null
+package jalview.fts.service.uniprot;
+
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.GFTSPanel;
+import jalview.gui.SequenceFetcher;
+import jalview.util.MessageManager;
+
+@SuppressWarnings("serial")
+public class UniprotFTSPanel extends GFTSPanel
+{
+
+
+ public UniprotFTSPanel(SequenceFetcher seqFetcher)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+ @Override
+ public void txt_search_ActionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void btn_ok_ActionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+
+ @Override
+ public FTSRestClientI getFTSRestClient()
+ {
+ return UniProtRestClient.getInstance();
+ }
+
+ @Override
+ public String getFTSFrameTitle()
+ {
+ return MessageManager.getString("label.uniprot_sequence_fetcher");
+ }
+
+}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
{
debounceTrap++;
String currentSelection = database.getSelectedItem();
- if (!currentSelection.equalsIgnoreCase("pdb"))
- {
- otherSourceAction();
- }
+
if (currentSelection.equalsIgnoreCase("pdb")
&& (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
{
pdbSourceAction();
}
+ else if (currentSelection.equalsIgnoreCase("uniprot")
+ && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ {
+ uniprotSourceAction();
+ }
+ else
+ {
+ otherSourceAction();
+ }
database.action = -1;
}
});
frame.dispose();
}
+ private void uniprotSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new UniprotFTSPanel(this);
+ frame.dispose();
+ }
private void otherSourceAction()
{
try
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- Collection<FTSDataColumnI> wantedFields = FTSDataColumnPreferences
- .getStructureSummaryFields();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
- pdbRestCleint = PDBFTSRestClient.getInstance();
FTSRestResponse resultList;
try
{
public void run()
{
long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = FTSDataColumnPreferences
- .getStructureSummaryFields();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq);
}
- pdbRestCleint = PDBFTSRestClient.getInstance();
FTSRestResponse resultList;
try
{
btn_cancel.setEnabled(false);
btn_view.setVisible(false);
btn_cancel.setVisible(false);
- previousWantedFields = FTSDataColumnPreferences
- .getStructureSummaryFields().toArray(
- new FTSDataColumnI[0]);
+ previousWantedFields = PDBFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns()
+ .toArray(new FTSDataColumnI[0]);
}
if (sourceTabbedPane.getTitleAt(index)
.equals(foundStructureSummary))
return true;
}
- return Arrays.equals(FTSDataColumnPreferences.getStructureSummaryFields()
+ return Arrays.equals(
+ PDBFTSRestClient.getInstance()
+ .getAllDefaulDisplayedDataColumns()
.toArray(new FTSDataColumnI[0]),
previousWantedFields) ? false : true;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
import java.io.BufferedReader;
import java.io.FileReader;
}
String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
- String actualResult = PDBFTSRestClient
+ String actualResult = PDBFTSRestClient.getInstance()
.getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
assertEquals("", expectedResult, actualResult);
git://source.jalview.org / jalview.git / commitdiff