-/* PDAP:PDTREE package for Mesquite copyright 2001-2010 P. Midford & W. MaddisonPDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html)*/package mesquite.pdap.Alog10TransformChar;import mesquite.lib.*;import mesquite.lib.characters.*;import mesquite.cont.lib.*;import mesquite.lib.table.*;/** ======================================================================== */public class Alog10TransformChar extends ContDataAlterer { static final double log10 = Math.log(10.0); static final double maxExp = Math.log(Double.MAX_VALUE)/log10; /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } /** Called to alter data in those cells selected in table*/ public boolean alterData(CharacterData data, MesquiteTable table, UndoReference undoReference){ boolean valid=true; boolean did=false; if (!(data instanceof ContinuousData)) return false; UndoInstructions undoInstructions = null; ContinuousData cData = (ContinuousData)data; if (table==null && data !=null){ // first check for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all cells are valid if (valid) { undoInstructions = data.getUndoInstructionsAllData(); for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { transformCell(cData, i, j); did=true; } } } } else if (table!=null && cData !=null){ if (table.anyCellSelected()) { // first check for (int i=0; i<table.getNumColumns(); i++) for (int j=0; j<table.getNumRows(); j++) if (table.isCellSelected(i,j)) { valid = valid && checkCell(cData, i, j); } // then transform only if all selected cells are valid if (valid) { undoInstructions = data.getUndoInstructionsAllData(); for (int i=0; i<table.getNumColumns(); i++) for (int j=0; j<table.getNumRows(); j++) if (table.isCellSelected(i,j)) { transformCell(cData, i, j); did = true; } } } else if (table.anyRowSelected()) { // first check for (int j=0; j<table.getNumRows(); j++) { if (table.isRowSelected(j)) for (int i=0; i<table.getNumColumns(); i++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all selected cells are valid if (valid) { undoInstructions = data.getUndoInstructionsAllData(); for (int j=0; j<table.getNumRows(); j++) { if (table.isRowSelected(j)) for (int i=0; i<table.getNumColumns(); i++) { transformCell(cData, i, j); did = true; } } } } else if (table.anyColumnSelected()) { // first check for (int i=0; i<table.getNumColumns(); i++){ if (table.isColumnSelected(i)) for (int j=0; j<table.getNumRows(); j++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all selected cells are valid if (valid) { undoInstructions = data.getUndoInstructionsAllData(); for (int i=0; i<table.getNumColumns(); i++){ if (table.isColumnSelected(i)) for (int j=0; j<table.getNumRows(); j++) { transformCell(cData, i, j); did=true; } } } } else { // first check for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { valid = valid && checkCell(cData, i, j); did=true; } } // then transform only if all selected cells are valid if (valid) { undoInstructions = data.getUndoInstructionsAllData(); for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { transformCell(cData, i, j); did=true; } } } } } if (undoInstructions!=null) { undoInstructions.setNewData(data); if (undoReference!=null){ undoReference.setUndoer(undoInstructions); undoReference.setResponsibleModule(this); } } if (!valid){ alert("Values were not alog 10 transformed because some values were too large."); } return did; } private boolean checkCell(ContinuousData data, int ic, int it){ int item = 0; //TODO: other items double state = data.getState(ic,it, item); if (MesquiteDouble.isCombinable(state)) return (state<=maxExp); else return true; //if not combinable, transformCell ignores it, so should checkCell } private void transformCell(ContinuousData data, int ic, int it){ int item = 0; //TODO: other items double state = data.getState(ic,it, item); if (MesquiteDouble.isCombinable(state)) { data.setState(ic,it, item, Math.exp(state*log10)); } } /*.................................................................................................................*/ /** returns a descriptive name for the module @return String */ public String getName() { return "Alog 10 transform"; } /*.................................................................................................................*/ /** returns a descriptive name for the module @return String */ public String getVersion() { return "1.15"; } /*.................................................................................................................*/ /** marks the module as NOT being a prerelease @return boolean - constant false */ public boolean isPrerelease() { return false; } /** marks the module as doing a substantive calculation - not decorative */ public boolean isSubstantive(){ return true; } /*.................................................................................................................*/ /** returns an explanation of what the module does. @return String */ public String getExplanation() { return "Alters continuous data by antilog base 10 transforming values." ; } }
+/* PDAP:PDTREE package for Mesquite copyright 2001-2010 P. Midford & W. MaddisonPDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html)*/package mesquite.pdap.Alog10TransformChar;import mesquite.lib.*;import mesquite.lib.characters.*;import mesquite.cont.lib.*;import mesquite.lib.table.*;/** ======================================================================== */public class Alog10TransformChar extends ContDataAlterer { static final double log10 = Math.log(10.0); static final double maxExp = Math.log(Double.MAX_VALUE)/log10; /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } /** Called to alter data in those cells selected in table*/ public boolean alterData(CharacterData data, MesquiteTable table, UndoReference undoReference){ boolean valid=true; boolean did=false; if (!(data instanceof ContinuousData)) return false; ContinuousData cData = (ContinuousData)data; if (table==null && data !=null){ // first check for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all cells are valid if (valid) { for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { transformCell(cData, i, j); did=true; } } } } else if (table!=null && cData !=null){ if (table.anyCellSelected()) { // first check for (int i=0; i<table.getNumColumns(); i++) for (int j=0; j<table.getNumRows(); j++) if (table.isCellSelected(i,j)) { valid = valid && checkCell(cData, i, j); } // then transform only if all selected cells are valid if (valid) { for (int i=0; i<table.getNumColumns(); i++) for (int j=0; j<table.getNumRows(); j++) if (table.isCellSelected(i,j)) { transformCell(cData, i, j); did = true; } } } else if (table.anyRowSelected()) { // first check for (int j=0; j<table.getNumRows(); j++) { if (table.isRowSelected(j)) for (int i=0; i<table.getNumColumns(); i++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all selected cells are valid if (valid) { for (int j=0; j<table.getNumRows(); j++) { if (table.isRowSelected(j)) for (int i=0; i<table.getNumColumns(); i++) { transformCell(cData, i, j); did = true; } } } } else if (table.anyColumnSelected()) { // first check for (int i=0; i<table.getNumColumns(); i++){ if (table.isColumnSelected(i)) for (int j=0; j<table.getNumRows(); j++) { valid = valid && checkCell(cData, i, j); } } // then transform only if all selected cells are valid if (valid) { for (int i=0; i<table.getNumColumns(); i++){ if (table.isColumnSelected(i)) for (int j=0; j<table.getNumRows(); j++) { transformCell(cData, i, j); did=true; } } } } else { // first check for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { valid = valid && checkCell(cData, i, j); did=true; } } // then transform only if all selected cells are valid if (valid) { for (int i=0; i<cData.getNumChars(); i++){ for (int j=0; j<cData.getNumTaxa(); j++) { transformCell(cData, i, j); did=true; } } } } } if (!valid){ alert("Values were not alog 10 transformed because some values were too large."); } return did; } private boolean checkCell(ContinuousData data, int ic, int it){ int item = 0; //TODO: other items double state = data.getState(ic,it, item); if (MesquiteDouble.isCombinable(state)) return (state<=maxExp); else return true; //if not combinable, transformCell ignores it, so should checkCell } private void transformCell(ContinuousData data, int ic, int it){ int item = 0; //TODO: other items double state = data.getState(ic,it, item); if (MesquiteDouble.isCombinable(state)) { data.setState(ic,it, item, Math.exp(state*log10)); } } /*.................................................................................................................*/ /** returns a descriptive name for the module @return String */ public String getName() { return "Alog 10 transform"; } /*.................................................................................................................*/ /** returns a descriptive name for the module @return String */ public String getVersion() { return "1.15"; } /*.................................................................................................................*/ /** marks the module as NOT being a prerelease @return boolean - constant false */ public boolean isPrerelease() { return false; } /** marks the module as doing a substantive calculation - not decorative */ public boolean isSubstantive(){ return true; } /*.................................................................................................................*/ /** returns an explanation of what the module does. @return String */ public String getExplanation() { return "Alters continuous data by antilog base 10 transforming values." ; } }
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