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java.lang.Objectorg.biojava.bio.structure.align.ce.StartupParameters
public class StartupParameters
a simple bean that contains the parameters that can get set at startup
Constructor Summary | |
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StartupParameters()
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Method Summary | |
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String |
getAlignPairs()
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String |
getFile1()
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String |
getFile2()
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int |
getMaxGapSize()
CE specific parameter: set the Max gap size parameter G (during AFP extension). |
Double |
getMaxOptRMSD()
(jCE specific): maximum RMSD that shall be calculated for the alignment. |
String |
getOutFile()
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String |
getPdb1()
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String |
getPdb2()
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String |
getPdbFilePath()
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String |
getSaveOutputDir()
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String |
getShowDBresult()
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boolean |
isAutoFetch()
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boolean |
isFlexible()
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boolean |
isOutputPDB()
When writing the results to a file, don;t write as XML but write aligned PDB file |
boolean |
isPdbDirSplit()
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boolean |
isPrintCE()
Display the output string in CE style |
boolean |
isPrintFatCat()
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boolean |
isPrintXML()
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boolean |
isShow3d()
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boolean |
isShowAFPRanges()
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boolean |
isShowMenu()
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void |
setAlignPairs(String alignPairs)
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void |
setAutoFetch(boolean autoFetch)
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void |
setFile1(String file1)
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void |
setFile2(String file2)
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void |
setFlexible(boolean flexible)
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void |
setMaxGapSize(int maxGapSize)
CE specific parameter: set the Max gap size parameter G (during AFP extension). |
void |
setMaxOptRMSD(Double maxOptRMSD)
(jCE specific): maximum RMSD that shall be calculated for the alignment. |
void |
setOutFile(String outFile)
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void |
setOutputPDB(boolean printPDB)
When writing the results to a file, don;t write as XML but write aligned PDB file |
void |
setPdb1(String pdb1)
mandatory argument to set the first PDB (and optionally chain ID) to be aligned. |
void |
setPdb2(String pdb2)
mandatory argument to set the second PDB (and optionally chain ID) to be aligned. |
void |
setPdbDirSplit(boolean pdbDirSplit)
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void |
setPdbFilePath(String pdbFilePath)
mandatory argument to set the location of PDB files. |
void |
setPrintCE(boolean printCE)
Display the output string in CE style |
void |
setPrintFatCat(boolean printFatCat)
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void |
setPrintXML(boolean printXML)
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void |
setSaveOutputDir(String saveOutputDir)
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void |
setShow3d(boolean show3d)
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void |
setShowAFPRanges(boolean showAFP)
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void |
setShowDBresult(String showDBresult)
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void |
setShowMenu(boolean showMenu)
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String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public StartupParameters()
Method Detail |
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public String toString()
toString
in class Object
public String getAlignPairs()
public void setAlignPairs(String alignPairs)
public String getSaveOutputDir()
public void setSaveOutputDir(String saveOutputDir)
public boolean isShowMenu()
public void setShowMenu(boolean showMenu)
public boolean isPrintCE()
public void setPrintCE(boolean printCE)
printCE
- a flagpublic boolean isFlexible()
public void setFlexible(boolean flexible)
public String getPdb1()
public void setPdb1(String pdb1)
pdb1
- public String getPdb2()
public void setPdb2(String pdb2)
pdb2
- public boolean isPdbDirSplit()
public void setPdbDirSplit(boolean pdbDirSplit)
public boolean isPrintXML()
public void setPrintXML(boolean printXML)
public boolean isPrintFatCat()
public void setPrintFatCat(boolean printFatCat)
public String getPdbFilePath()
public void setPdbFilePath(String pdbFilePath)
pdbFilePath
- public boolean isShow3d()
public void setShow3d(boolean show3d)
public String getOutFile()
public void setOutFile(String outFile)
public boolean isAutoFetch()
public void setAutoFetch(boolean autoFetch)
public String getShowDBresult()
public void setShowDBresult(String showDBresult)
public int getMaxGapSize()
public void setMaxGapSize(int maxGapSize)
maxGapSize
- public String getFile1()
public void setFile1(String file1)
public String getFile2()
public void setFile2(String file2)
public boolean isShowAFPRanges()
public void setShowAFPRanges(boolean showAFP)
public boolean isOutputPDB()
public void setOutputPDB(boolean printPDB)
printPDB
- flag to print aligned PDBpublic Double getMaxOptRMSD()
public void setMaxOptRMSD(Double maxOptRMSD)
maxOptRMSD
- max RMSD to calculate
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