+++ /dev/null
-/**
- * Author: Andreas Wilm
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-/**
- * Changes:
- * 2007-12-12: Andreas Wilm (UCD): initial implementation
- *
- */
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-
-#include <iostream>
-#include <vector>
-#include "clustalw_version.h"
-#include "Help.h"
-
-using namespace std;
-
-
-Help::Help()
-{
- section s;
- string version = CLUSTALW_VERSION;
-
- // all sections were added in order of appearance in original
- // clustalw_help
-
- // To add new entries use the template below.
- // Paste content as text,
- // escape all " with \",
- // add " at the beginning of the line,
- // and \n" at the end of the line
- // template:
- // s.marker = "";
- // s.title = "";
- // s.content = "";
- // sections.push_back(s);
-
- s.marker = "NEW";
- s.title = "NEW FEATURES/OPTIONS";
- s.content = "==UPGMA=="
-" \n"
-" The UPGMA algorithm has been added to allow faster tree construction. The user now\n"
-" has the choice of using Neighbour Joining or UPGMA. The default is still NJ, but the\n"
-" user can change this by setting the clustering parameter.\n"
-" \n"
-" -CLUSTERING= :NJ or UPGMA\n"
-" \n"
-"==ITERATION==\n"
-"\n"
-" A remove first iteration scheme has been added. This can be used to improve the final\n"
-" alignment or improve the alignment at each stage of the progressive alignment. During the \n"
-" iteration step each sequence is removed in turn and realigned. If the resulting alignment \n"
-" is better than the previous alignment it is kept. This process is repeated until the score\n"
-" converges (the score is not improved) or until the maximum number of iterations is \n"
-" reached. The user can iterate at each step of the progressive alignment by setting the \n"
-" iteration parameter to TREE or just on the final alignment by seting the iteration \n"
-" parameter to ALIGNMENT. The default is no iteration. The maximum number of iterations can \n"
-" be set using the numiter parameter. The default number of iterations is 3.\n"
-" \n"
-" -ITERATION= :NONE or TREE or ALIGNMENT\n"
-" \n"
-" -NUMITER=n :Maximum number of iterations to perform\n"
-" \n"
-"==HELP==\n"
-" \n"
-" -FULLHELP :Print out the complete help content\n"
-" \n"
-"==MISC==\n"
-"\n"
-" -MAXSEQLEN=n :Maximum allowed sequence length\n"
-" \n"
-" -QUIET :Reduce console output to minimum\n"
-" \n"
-" -STATS=file :Log some alignents statistics to file\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "1";
- s.title = "General help for CLUSTAL W (" + version + ")";
- s.content = "Clustal W is a general purpose multiple alignment program for DNA or proteins.\n"
-"\n"
-"SEQUENCE INPUT: all sequences must be in 1 file, one after another. \n"
-"7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT, \n"
-"Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.\n"
-"All non-alphabetic characters (spaces, digits, punctuation marks) are ignored\n"
-"except \"-\" which is used to indicate a GAP (\".\" in MSF-RSF). \n"
-"\n"
-"To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to \n"
-"INPUT them; go to menu item 2 to do the multiple alignment.\n"
-"\n"
-"PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments. Use this to\n"
-"add a new sequence to an old alignment, or to use secondary structure to guide \n"
-"the alignment process. GAPS in the old alignments are indicated using the \"-\" \n"
-"character. PROFILES can be input in ANY of the allowed formats; just \n"
-"use \"-\" (or \".\" for MSF-RSF) for each gap position.\n"
-"\n"
-"PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in\n"
-"with \"-\" characters to indicate gaps) OR after a multiple alignment while the \n"
-"alignment is still in memory.\n"
-"\n"
-"\n"
-"The program tries to automatically recognise the different file formats used\n"
-"and to guess whether the sequences are amino acid or nucleotide. This is not\n"
-"always foolproof.\n"
-"\n"
-"FASTA and NBRF-PIR formats are recognised by having a \">\" as the first \n"
-"character in the file. \n"
-"\n"
-"EMBL-Swiss Prot formats are recognised by the letters\n"
-"ID at the start of the file (the token for the entry name field). \n"
-"\n"
-"CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.\n"
-"\n"
-"GCG-MSF format is recognised by one of the following:\n"
-" - the word PileUp at the start of the file. \n"
-" - the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT\n"
-" at the start of the file.\n"
-" - the word MSF on the first line of the line, and the characters ..\n"
-" at the end of this line.\n"
-"\n"
-"GCG-RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of\n"
-"the file.\n"
-"\n"
-"\n"
-"If 85% or more of the characters in the sequence are from A,C,G,T,U or N, the\n"
-"sequence will be assumed to be nucleotide. This works in 97.3% of cases\n"
-"but watch out!\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "2";
- s.title = "Help for multiple alignments";
- s.content = "If you have already loaded sequences, use menu item 1 to do the complete\n"
-"multiple alignment. You will be prompted for 2 output files: 1 for the \n"
-"alignment itself; another to store a dendrogram that describes the similarity\n"
-"of the sequences to each other.\n"
-"\n"
-"Multiple alignments are carried out in 3 stages (automatically done from menu\n"
-"item 1 ...Do complete multiple alignments now):\n"
-"\n"
-"1) all sequences are compared to each other (pairwise alignments);\n"
-"\n"
-"2) a dendrogram (like a phylogenetic tree) is constructed, describing the\n"
-"approximate groupings of the sequences by similarity (stored in a file).\n"
-"\n"
-"3) the final multiple alignment is carried out, using the dendrogram as a guide.\n"
-"\n"
-"\n"
-"PAIRWISE ALIGNMENT parameters control the speed-sensitivity of the initial\n"
-"alignments.\n"
-"\n"
-"MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments.\n"
-"\n"
-"\n"
-"RESET GAPS (menu item 7) will remove any new gaps introduced into the sequences\n"
-"during multiple alignment if you wish to change the parameters and try again.\n"
-"This only takes effect just before you do a second multiple alignment. You\n"
-"can make phylogenetic trees after alignment whether or not this is ON.\n"
-"If you turn this OFF, the new gaps are kept even if you do a second multiple\n"
-"alignment. This allows you to iterate the alignment gradually. Sometimes, the \n"
-"alignment is improved by a second or third pass.\n"
-"\n"
-"SCREEN DISPLAY (menu item 8) can be used to send the output alignments to the \n"
-"screen as well as to the output file.\n"
-"\n"
-"You can skip the first stages (pairwise alignments; dendrogram) by using an\n"
-"old dendrogram file (menu item 3); or you can just produce the dendrogram\n"
-"with no final multiple alignment (menu item 2).\n"
-"\n"
-"\n"
-"OUTPUT FORMAT: Menu item 9 (format options) allows you to choose from 6 \n"
-"different alignment formats (CLUSTAL, GCG, NBRF-PIR, PHYLIP, GDE, NEXUS, and FASTA). \n"
-"\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "3";
- s.title = "Help for pairwise alignment parameters";
- s.content = "A distance is calculated between every pair of sequences and these are used to\n"
-"construct the dendrogram which guides the final multiple alignment. The scores\n"
-"are calculated from separate pairwise alignments. These can be calculated using\n"
-"2 methods: dynamic programming (slow but accurate) or by the method of Wilbur\n"
-"and Lipman (extremely fast but approximate). \n"
-"\n"
-"You can choose between the 2 alignment methods using menu option 8. The\n"
-"slow-accurate method is fine for short sequences but will be VERY SLOW for \n"
-"many (e.g. >100) long (e.g. >1000 residue) sequences. \n"
-"\n"
-"SLOW-ACCURATE alignment parameters:\n"
-" These parameters do not have any affect on the speed of the alignments. \n"
-"They are used to give initial alignments which are then rescored to give percent\n"
-"identity scores. These % scores are the ones which are displayed on the \n"
-"screen. The scores are converted to distances for the trees.\n"
-"\n"
-"1) Gap Open Penalty: the penalty for opening a gap in the alignment.\n"
-"2) Gap extension penalty: the penalty for extending a gap by 1 residue.\n"
-"3) Protein weight matrix: the scoring table which describes the similarity\n"
-" of each amino acid to each other.\n"
-"4) DNA weight matrix: the scores assigned to matches and mismatches \n"
-" (including IUB ambiguity codes).\n"
-"\n"
-"\n"
-"FAST-APPROXIMATE alignment parameters:\n"
-"\n"
-"These similarity scores are calculated from fast, approximate, global align-\n"
-"ments, which are controlled by 4 parameters. 2 techniques are used to make\n"
-"these alignments very fast: 1) only exactly matching fragments (k-tuples) are\n"
-"considered; 2) only the 'best' diagonals (the ones with most k-tuple matches)\n"
-"are used.\n"
-"\n"
-"K-TUPLE SIZE: This is the size of exactly matching fragment that is used. \n"
-"INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity.\n"
-"For longer sequences (e.g. >1000 residues) you may need to increase the default.\n"
-"\n"
-"GAP PENALTY: This is a penalty for each gap in the fast alignments. It has\n"
-"little affect on the speed or sensitivity except for extreme values.\n"
-"\n"
-"TOP DIAGONALS: The number of k-tuple matches on each diagonal (in an imaginary\n"
-"dot-matrix plot) is calculated. Only the best ones (with most matches) are\n"
-"used in the alignment. This parameter specifies how many. Decrease for speed;\n"
-"increase for sensitivity.\n"
-"\n"
-"WINDOW SIZE: This is the number of diagonals around each of the 'best' \n"
-"diagonals that will be used. Decrease for speed; increase for sensitivity.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "4";
- s.title = "Help for multiple alignment parameters";
- s.content = "These parameters control the final multiple alignment. This is the core of the\n"
-"program and the details are complicated. To fully understand the use of the\n"
-"parameters and the scoring system, you will have to refer to the documentation.\n"
-"\n"
-"Each step in the final multiple alignment consists of aligning two alignments \n"
-"or sequences. This is done progressively, following the branching order in \n"
-"the GUIDE TREE. The basic parameters to control this are two gap penalties and\n"
-"the scores for various identical-non-indentical residues. \n"
-"\n"
-"1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the \n"
-"cost of opening up every new gap and the cost of every item in a gap. \n"
-"Increasing the gap opening penalty will make gaps less frequent. Increasing \n"
-"the gap extension penalty will make gaps shorter. Terminal gaps are not \n"
-"penalised.\n"
-"\n"
-"3) The DELAY DIVERGENT SEQUENCES switch delays the alignment of the most\n"
-"distantly related sequences until after the most closely related sequences have \n"
-"been aligned. The setting shows the percent identity level required to delay\n"
-"the addition of a sequence; sequences that are less identical than this level\n"
-"to any other sequences will be aligned later.\n"
-"\n"
-"\n"
-"\n"
-"4) The TRANSITION WEIGHT gives transitions (A <--> G or C <--> T \n"
-"i.e. purine-purine or pyrimidine-pyrimidine substitutions) a weight between 0\n"
-"and 1; a weight of zero means that the transitions are scored as mismatches,\n"
-"while a weight of 1 gives the transitions the match score. For distantly related\n"
-"DNA sequences, the weight should be near to zero; for closely related sequences\n"
-"it can be useful to assign a higher score.\n"
-"\n"
-"\n"
-"5) PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of\n"
-"weight matrices. The default for proteins in version 1.8 is the PAM series \n"
-"derived by Gonnet and colleagues. Note, a series is used! The actual matrix\n"
-"that is used depends on how similar the sequences to be aligned at this \n"
-"alignment step are. Different matrices work differently at each evolutionary\n"
-"distance. \n"
-"\n"
-"6) DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series)\n"
-"can be selected. The default is the matrix used by BESTFIT for comparison of\n"
-"nucleic acid sequences.\n"
-"\n"
-"Further help is offered in the weight matrix menu.\n"
-"\n"
-"\n"
-"7) In the weight matrices, you can use negative as well as positive values if\n"
-"you wish, although the matrix will be automatically adjusted to all positive\n"
-"scores, unless the NEGATIVE MATRIX option is selected.\n"
-"\n"
-"8) PROTEIN GAP PARAMETERS displays a menu allowing you to set some Gap Penalty\n"
-"options which are only used in protein alignments.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "A";
- s.title = "Help for protein gap parameters.";
- s.content = "1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce\n"
-"or increase the gap opening penalties at each position in the alignment or\n"
-"sequence. See the documentation for details. As an example, positions that \n"
-"are rich in glycine are more likely to have an adjacent gap than positions that\n"
-"are rich in valine.\n"
-"\n"
-"2) 3) HYDROPHILIC GAP PENALTIES are used to increase the chances of a gap within\n"
-"a run (5 or more residues) of hydrophilic amino acids; these are likely to\n"
-"be loop or random coil regions where gaps are more common. The residues that \n"
-"are \"considered\" to be hydrophilic are set by menu item 3.\n"
-"\n"
-"4) GAP SEPARATION DISTANCE tries to decrease the chances of gaps being too\n"
-"close to each other. Gaps that are less than this distance apart are penalised\n"
-"more than other gaps. This does not prevent close gaps; it makes them less\n"
-"frequent, promoting a block-like appearance of the alignment.\n"
-"\n"
-"5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes\n"
-"of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above).\n"
-"If you turn this off, end gaps will be ignored for this purpose. This is\n"
-"useful when you wish to align fragments where the end gaps are not biologically\n"
-"meaningful.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "5";
- s.title = "Help for output format options.";
- s.content = "Six output formats are offered. You can choose any (or all 6 if you wish). \n"
-"\n"
-"CLUSTAL format output is a self explanatory alignment format. It shows the\n"
-"sequences aligned in blocks. It can be read in again at a later date to\n"
-"(for example) calculate a phylogenetic tree or add a new sequence with a \n"
-"profile alignment.\n"
-"\n"
-"GCG output can be used by any of the GCG programs that can work on multiple\n"
-"alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG\n"
-".msf format files (multiple sequence file); new in version 7 of GCG.\n"
-"\n"
-"PHYLIP format output can be used for input to the PHYLIP package of Joe \n"
-"Felsenstein. This is an extremely widely used package for doing every \n"
-"imaginable form of phylogenetic analysis (MUCH more than the the modest intro-\n"
-"duction offered by this program).\n"
-"\n"
-"NBRF-PIR: this is the same as the standard PIR format with ONE ADDITION. Gap\n"
-"characters \"-\" are used to indicate the positions of gaps in the multiple \n"
-"alignment. These files can be re-used as input in any part of clustal that\n"
-"allows sequences (or alignments or profiles) to be read in. \n"
-"\n"
-"GDE: this is the flat file format used by the GDE package of Steven Smith.\n"
-"\n"
-"NEXUS: the format used by several phylogeny programs, including PAUP and\n"
-"MacClade.\n"
-"\n"
-"GDE OUTPUT CASE: sequences in GDE format may be written in either upper or\n"
-"lower case.\n"
-"\n"
-"CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the\n"
-"alignment lines in clustalw format.\n"
-"\n"
-"OUTPUT ORDER is used to control the order of the sequences in the output\n"
-"alignments. By default, the order corresponds to the order in which the\n"
-"sequences were aligned (from the guide tree-dendrogram), thus automatically\n"
-"grouping closely related sequences. This switch can be used to set the order\n"
-"to the same as the input file.\n"
-"\n"
-"PARAMETER OUTPUT: This option allows you to save all your parameter settings\n"
-"in a parameter file. This file can be used subsequently to rerun Clustal W\n"
-"using the same parameters.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "6";
- s.title = "Help for profile and structure alignments";
- s.content = "By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile \n"
-"alignments allow you to store alignments of your favourite sequences and add\n"
-"new sequences to them in small bunches at a time. A profile is simply an\n"
-"alignment of one or more sequences (e.g. an alignment output file from CLUSTAL\n"
-"W). Each input can be a single sequence. One or both sets of input sequences\n"
-"may include secondary structure assignments or gap penalty masks to guide the\n"
-"alignment. \n"
-"\n"
-"The profiles can be in any of the allowed input formats with \"-\" characters\n"
-"used to specify gaps (except for MSF-RSF where \".\" is used).\n"
-"\n"
-"You have to specify the 2 profiles by choosing menu items 1 and 2 and giving\n"
-"2 file names. Then Menu item 3 will align the 2 profiles to each other. \n"
-"Secondary structure masks in either profile can be used to guide the alignment.\n"
-"\n"
-"Menu item 4 will take the sequences in the second profile and align them to\n"
-"the first profile, 1 at a time. This is useful to add some new sequences to\n"
-"an existing alignment, or to align a set of sequences to a known structure. \n"
-"In this case, the second profile would not be pre-aligned.\n"
-"\n"
-"\n"
-"The alignment parameters can be set using menu items 5, 6 and 7. These are\n"
-"EXACTLY the same parameters as used by the general, automatic multiple\n"
-"alignment procedure. The general multiple alignment procedure is simply a\n"
-"series of profile alignments. Carrying out a series of profile alignments on\n"
-"larger and larger groups of sequences, allows you to manually build up a\n"
-"complete alignment, if necessary editing intermediate alignments.\n"
-"\n"
-"SECONDARY STRUCTURE OPTIONS. Menu Option 0 allows you to set 2D structure\n"
-"parameters. If a solved structure is available, it can be used to guide the \n"
-"alignment by raising gap penalties within secondary structure elements, so \n"
-"that gaps will preferentially be inserted into unstructured surface loops.\n"
-"Alternatively, a user-specified gap penalty mask can be supplied directly.\n"
-"\n"
-"A gap penalty mask is a series of numbers between 1 and 9, one per position in \n"
-"the alignment. Each number specifies how much the gap opening penalty is to be \n"
-"raised at that position (raised by multiplying the basic gap opening penalty\n"
-"by the number) i.e. a mask figure of 1 at a position means no change\n"
-"in gap opening penalty; a figure of 4 means that the gap opening penalty is\n"
-"four times greater at that position, making gaps 4 times harder to open.\n"
-"\n"
-"The format for gap penalty masks and secondary structure masks is explained\n"
-"in the help under option 0 (secondary structure options).\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "B";
- s.title = "Help for secondary structure - gap penalty masks";
- s.content = "The use of secondary structure-based penalties has been shown to improve the\n"
-"accuracy of multiple alignment. Therefore CLUSTAL W now allows gap penalty \n"
-"masks to be supplied with the input sequences. The masks work by raising gap \n"
-"penalties in specified regions (typically secondary structure elements) so that\n"
-"gaps are preferentially opened in the less well conserved regions (typically \n"
-"surface loops).\n"
-"\n"
-"Options 1 and 2 control whether the input secondary structure information or\n"
-"gap penalty masks will be used.\n"
-"\n"
-"Option 3 controls whether the secondary structure and gap penalty masks should\n"
-"be included in the output alignment.\n"
-"\n"
-"Options 4 and 5 provide the value for raising the gap penalty at core Alpha \n"
-"Helical (A) and Beta Strand (B) residues. In CLUSTAL format, capital residues \n"
-"denote the A and B core structure notation. The basic gap penalties are\n"
-"multiplied by the amount specified.\n"
-"\n"
-"Option 6 provides the value for the gap penalty in Loops. By default this \n"
-"penalty is not raised. In CLUSTAL format, loops are specified by \".\" in the \n"
-"secondary structure notation.\n"
-"\n"
-"Option 7 provides the value for setting the gap penalty at the ends of \n"
-"secondary structures. Ends of secondary structures are observed to grow \n"
-"and-or shrink in related structures. Therefore by default these are given \n"
-"intermediate values, lower than the core penalties. All secondary structure \n"
-"read in as lower case in CLUSTAL format gets the reduced terminal penalty.\n"
-"\n"
-"Options 8 and 9 specify the range of structure termini for the intermediate \n"
-"penalties. In the alignment output, these are indicated as lower case. \n"
-"For Alpha Helices, by default, the range spans the end helical turn. For \n"
-"Beta Strands, the default range spans the end residue and the adjacent loop \n"
-"residue, since sequence conservation often extends beyond the actual H-bonded\n"
-"Beta Strand.\n"
-"\n"
-"CLUSTAL W can read the masks from SWISS-PROT, CLUSTAL or GDE format input\n"
-"files. For many 3-D protein structures, secondary structure information is\n"
-"recorded in the feature tables of SWISS-PROT database entries. You should\n"
-"always check that the assignments are correct - some are quite inaccurate.\n"
-"CLUSTAL W looks for SWISS-PROT HELIX and STRAND assignments e.g.\n"
-"\n"
-"FT HELIX 100 115\n"
-"FT STRAND 118 119\n"
-"\n"
-"The structure and penalty masks can also be read from CLUSTAL alignment format \n"
-"as comment lines beginning \"!SS_\" or \"!GM_\" e.g.\n"
-"\n"
-"!SS_HBA_HUMA ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA\n"
-"!GM_HBA_HUMA 112224444444444222122244444444442222224222111111111222444444\n"
-"HBA_HUMA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK\n"
-"\n"
-"Note that the mask itself is a set of numbers between 1 and 9 each of which is \n"
-"assigned to the residue(s) in the same column below. \n"
-"\n"
-"In GDE flat file format, the masks are specified as text and the names must\n"
-"begin with \"SS_ or \"GM_.\n"
-"\n"
-"Either a structure or penalty mask or both may be used. If both are included in\n"
-"an alignment, the user will be asked which is to be used.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "C";
- s.title = "Help for secondary structure - gap penalty mask output options";
- s.content = "The options in this menu let you choose whether or not to include the masks\n"
-"in the CLUSTAL W output alignments. Showing both is useful for understanding\n"
-"how the masks work. The secondary structure information is itself very useful\n"
-"in judging the alignment quality and in seeing how residue conservation\n"
-"patterns vary with secondary structure.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "7";
- s.title = "Help for phylogenetic trees";
- s.content = "1) Before calculating a tree, you must have an ALIGNMENT in memory. This can be\n"
-"input in any format or you should have just carried out a full multiple\n"
-"alignment and the alignment is still in memory. \n"
-"\n"
-"\n"
-"*************** Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! ***************\n"
-"\n"
-"\n"
-"The methods used are NJ (Neighbour Joining) and UPGMA. First\n"
-"you calculate distances (percent divergence) between all pairs of sequence from\n"
-"a multiple alignment; second you apply the NJ or UPGMA method to the distance matrix.\n"
-"\n"
-"2) EXCLUDE POSITIONS WITH GAPS? With this option, any alignment positions where\n"
-"ANY of the sequences have a gap will be ignored. This means that 'like' will be\n"
-"compared to 'like' in all distances, which is highly desirable. It also\n"
-"automatically throws away the most ambiguous parts of the alignment, which are\n"
-"concentrated around gaps (usually). The disadvantage is that you may throw away\n"
-"much of the data if there are many gaps (which is why it is difficult for us to\n"
-"make it the default). \n"
-"\n"
-"\n"
-"\n"
-"3) CORRECT FOR MULTIPLE SUBSTITUTIONS? For small divergence (say <10%) this\n"
-"option makes no difference. For greater divergence, it corrects for the fact\n"
-"that observed distances underestimate actual evolutionary distances. This is\n"
-"because, as sequences diverge, more than one substitution will happen at many\n"
-"sites. However, you only see one difference when you look at the present day\n"
-"sequences. Therefore, this option has the effect of stretching branch lengths\n"
-"in trees (especially long branches). The corrections used here (for DNA or\n"
-"proteins) are both due to Motoo Kimura. See the documentation for details. \n"
-"\n"
-"Where possible, this option should be used. However, for VERY divergent\n"
-"sequences, the distances cannot be reliably corrected. You will be warned if\n"
-"this happens. Even if none of the distances in a data set exceed the reliable\n"
-"threshold, if you bootstrap the data, some of the bootstrap distances may\n"
-"randomly exceed the safe limit. \n"
-"\n"
-"4) To calculate a tree, use option 4 (DRAW TREE NOW). This gives an UNROOTED\n"
-"tree and all branch lengths. The root of the tree can only be inferred by\n"
-"using an outgroup (a sequence that you are certain branches at the outside\n"
-"of the tree .... certain on biological grounds) OR if you assume a degree\n"
-"of constancy in the 'molecular clock', you can place the root in the 'middle'\n"
-"of the tree (roughly equidistant from all tips).\n"
-"\n"
-"5) TOGGLE PHYLIP BOOTSTRAP POSITIONS\n"
-"By default, the bootstrap values are correctly placed on the tree branches of\n"
-"the phylip format output tree. The toggle allows them to be placed on the\n"
-"nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView\n"
-"and Phylowin) only support node labelling but not branch labelling. Care\n"
-"should be taken to note which branches and labels go together.\n"
-"\n"
-"6) OUTPUT FORMATS: four different formats are allowed. None of these displays\n"
-"the tree visually. Useful display programs accepting PHYLIP format include\n"
-"NJplot (from Manolo Gouy and supplied with Clustal W), TreeView (Mac-PC), and\n"
-"PHYLIP itself - OR get the PHYLIP package and use the tree drawing facilities\n"
-"there. (Get the PHYLIP package anyway if you are interested in trees). The\n"
-"NEXUS format can be read into PAUP or MacClade.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "8";
- s.title = "Help for choosing a weight matrix";
- s.content = "For protein alignments, you use a weight matrix to determine the similarity of\n"
-"non-identical amino acids. For example, Tyr aligned with Phe is usually judged \n"
-"to be 'better' than Tyr aligned with Pro.\n"
-"\n"
-"There are three 'in-built' series of weight matrices offered. Each consists of\n"
-"several matrices which work differently at different evolutionary distances. To\n"
-"see the exact details, read the documentation. Crudely, we store several\n"
-"matrices in memory, spanning the full range of amino acid distance (from almost\n"
-"identical sequences to highly divergent ones). For very similar sequences, it\n"
-"is best to use a strict weight matrix which only gives a high score to\n"
-"identities and the most favoured conservative substitutions. For more divergent\n"
-"sequences, it is appropriate to use \"softer\" matrices which give a high score\n"
-"to many other frequent substitutions.\n"
-"\n"
-"1) BLOSUM (Henikoff). These matrices appear to be the best available for \n"
-"carrying out database similarity (homology searches). The matrices used are:\n"
-"Blosum 80, 62, 45 and 30. (BLOSUM was the default in earlier Clustal W\n"
-"versions)\n"
-"\n"
-"2) PAM (Dayhoff). These have been extremely widely used since the late '70s.\n"
-"We use the PAM 20, 60, 120 and 350 matrices.\n"
-"\n"
-"3) GONNET. These matrices were derived using almost the same procedure as the\n"
-"Dayhoff one (above) but are much more up to date and are based on a far larger\n"
-"data set. They appear to be more sensitive than the Dayhoff series. We use the\n"
-"GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for\n"
-"Clustal W version 1.8.\n"
-"\n"
-"We also supply an identity matrix which gives a score of 1.0 to two identical \n"
-"amino acids and a score of zero otherwise. This matrix is not very useful.\n"
-"Alternatively, you can read in your own (just one matrix, not a series).\n"
-"\n"
-"A new matrix can be read from a file on disk, if the filename consists only\n"
-"of lower case characters. The values in the new weight matrix must be integers\n"
-"and the scores should be similarities. You can use negative as well as positive\n"
-"values if you wish, although the matrix will be automatically adjusted to all\n"
-"positive scores.\n"
-"\n"
-"\n"
-"\n"
-"For DNA, a single matrix (not a series) is used. Two hard-coded matrices are \n"
-"available:\n"
-"\n"
-"\n"
-"1) IUB. This is the default scoring matrix used by BESTFIT for the comparison\n"
-"of nucleic acid sequences. X's and N's are treated as matches to any IUB\n"
-"ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0.\n"
-" \n"
-" \n"
-"2) CLUSTALW(1.6). The previous system used by Clustal W, in which matches score\n"
-"1.0 and mismatches score 0. All matches for IUB symbols also score 0.\n"
-"\n"
-"INPUT FORMAT The format used for a new matrix is the same as the BLAST program.\n"
-"Any lines beginning with a # character are assumed to be comments. The first\n"
-"non-comment line should contain a list of amino acids in any order, using the\n"
-"1 letter code, followed by a * character. This should be followed by a square\n"
-"matrix of integer scores, with one row and one column for each amino acid. The\n"
-"last row and column of the matrix (corresponding to the * character) contain\n"
-"the minimum score over the whole matrix.\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "9";
- s.title = "Help for command line parameters";
- s.content = " DATA (sequences)\n"
-"\n"
-"-INFILE=file.ext :input sequences.\n"
-"-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment).\n"
-"\n"
-"\n"
-" VERBS (do things)\n"
-"\n"
-"-OPTIONS :list the command line parameters\n"
-"-HELP or -CHECK :outline the command line params.\n"
-"-FULLHELP :output full help content.\n"
-"-ALIGN :do full multiple alignment.\n"
-"-TREE :calculate NJ tree.\n"
-"-PIM :output percent identity matrix (while calculating the tree)\n"
-"-BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).\n"
-"-CONVERT :output the input sequences in a different file format.\n"
-"\n"
-"\n"
-" PARAMETERS (set things)\n"
-"\n"
-"***General settings:****\n"
-"-INTERACTIVE :read command line, then enter normal interactive menus\n"
-"-QUICKTREE :use FAST algorithm for the alignment guide tree\n"
-"-TYPE= :PROTEIN or DNA sequences\n"
-"-NEGATIVE :protein alignment with negative values in matrix\n"
-"-OUTFILE= :sequence alignment file name\n"
-"-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS\n"
-"-OUTORDER= :INPUT or ALIGNED\n"
-"-CASE :LOWER or UPPER (for GDE output only)\n"
-"-SEQNOS= :OFF or ON (for Clustal output only)\n"
-"-SEQNO_RANGE=:OFF or ON (NEW: for all output formats)\n"
-"-RANGE=m,n :sequence range to write starting m to m+n\n"
-"-MAXSEQLEN=n :maximum allowed input sequence length\n"
-"-QUIET :Reduce console output to minimum\n"
-"-STATS= :Log some alignents statistics to file\n"
-"\n"
-"***Fast Pairwise Alignments:***\n"
-"-KTUPLE=n :word size\n"
-"-TOPDIAGS=n :number of best diags.\n"
-"-WINDOW=n :window around best diags.\n"
-"-PAIRGAP=n :gap penalty\n"
-"-SCORE :PERCENT or ABSOLUTE\n"
-"\n"
-"\n"
-"***Slow Pairwise Alignments:***\n"
-"-PWMATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename\n"
-"-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename\n"
-"-PWGAPOPEN=f :gap opening penalty \n"
-"-PWGAPEXT=f :gap opening penalty\n"
-"\n"
-"\n"
-"***Multiple Alignments:***\n"
-"-NEWTREE= :file for new guide tree\n"
-"-USETREE= :file for old guide tree\n"
-"-MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename\n"
-"-DNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename\n"
-"-GAPOPEN=f :gap opening penalty \n"
-"-GAPEXT=f :gap extension penalty\n"
-"-ENDGAPS :no end gap separation pen. \n"
-"-GAPDIST=n :gap separation pen. range\n"
-"-NOPGAP :residue-specific gaps off \n"
-"-NOHGAP :hydrophilic gaps off\n"
-"-HGAPRESIDUES= :list hydrophilic res. \n"
-"-MAXDIV=n :% ident. for delay\n"
-"-TYPE= :PROTEIN or DNA\n"
-"-TRANSWEIGHT=f :transitions weighting\n"
-"-ITERATION= :NONE or TREE or ALIGNMENT\n"
-"-NUMITER=n :maximum number of iterations to perform\n"
-"-NOWEIGHTS :disable sequence weighting\n"
-"\n"
-"\n"
-"***Profile Alignments:***\n"
-"-PROFILE :Merge two alignments by profile alignment\n"
-"-NEWTREE1= :file for new guide tree for profile1\n"
-"-NEWTREE2= :file for new guide tree for profile2\n"
-"-USETREE1= :file for old guide tree for profile1\n"
-"-USETREE2= :file for old guide tree for profile2\n"
-"\n"
-"\n"
-"***Sequence to Profile Alignments:***\n"
-"-SEQUENCES :Sequentially add profile2 sequences to profile1 alignment\n"
-"-NEWTREE= :file for new guide tree\n"
-"-USETREE= :file for old guide tree\n"
-"\n"
-"\n"
-"***Structure Alignments:***\n"
-"-NOSECSTR1 :do not use secondary structure-gap penalty mask for profile 1 \n"
-"-NOSECSTR2 :do not use secondary structure-gap penalty mask for profile 2\n"
-"-SECSTROUT=STRUCTURE or MASK or BOTH or NONE :output in alignment file\n"
-"-HELIXGAP=n :gap penalty for helix core residues \n"
-"-STRANDGAP=n :gap penalty for strand core residues\n"
-"-LOOPGAP=n :gap penalty for loop regions\n"
-"-TERMINALGAP=n :gap penalty for structure termini\n"
-"-HELIXENDIN=n :number of residues inside helix to be treated as terminal\n"
-"-HELIXENDOUT=n :number of residues outside helix to be treated as terminal\n"
-"-STRANDENDIN=n :number of residues inside strand to be treated as terminal\n"
-"-STRANDENDOUT=n:number of residues outside strand to be treated as terminal \n"
-"\n"
-"\n"
-"***Trees:***\n"
-"-OUTPUTTREE=nj OR phylip OR dist OR nexus\n"
-"-SEED=n :seed number for bootstraps.\n"
-"-KIMURA :use Kimura's correction. \n"
-"-TOSSGAPS :ignore positions with gaps.\n"
-"-BOOTLABELS=node OR branch :position of bootstrap values in tree display\n"
-"-CLUSTERING= :NJ or UPGMA\n"
-"";
- sections.push_back(s);
-
-
- s.marker = "0";
- s.title = "Help for tree output format options";
- s.content = "Four output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances\n"
-"4) Nexus\n"
-"\n"
-"None of these formats displays the results graphically. Many packages can\n"
-"display trees in the the PHYLIP format 2) below. It can also be imported into\n"
-"the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM for graphical display. \n"
-"NEXUS format trees can be read by PAUP and MacClade.\n"
-"\n"
-"1) Clustal format output. \n"
-"This format is verbose and lists all of the distances between the sequences and\n"
-"the number of alignment positions used for each. The tree is described at the\n"
-"end of the file. It lists the sequences that are joined at each alignment step\n"
-"and the branch lengths. After two sequences are joined, it is referred to later\n"
-"as a NODE. The number of a NODE is the number of the lowest sequence in that\n"
-"NODE. \n"
-"\n"
-"2) Phylip format output.\n"
-"This format is the New Hampshire format, used by many phylogenetic analysis\n"
-"packages. It consists of a series of nested parentheses, describing the\n"
-"branching order, with the sequence names and branch lengths. It can be used by\n"
-"the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the\n"
-"trees graphically. This is the same format used during multiple alignment for\n"
-"the guide trees. \n"
-"\n"
-"Use this format with NJplot (Manolo Gouy), supplied with Clustal W. Some other\n"
-"packages that can read and display New Hampshire format are TreeView (Mac/PC),\n"
-"TreeTool (UNIX), and Phylowin.\n"
-"\n"
-"3) The distances only.\n"
-"This format just outputs a matrix of all the pairwise distances in a format\n"
-"that can be used by the Phylip package. It used to be useful when one could not\n"
-"produce distances from protein sequences in the Phylip package but is now\n"
-"redundant (Protdist of Phylip 3.5 now does this).\n"
-"\n"
-"4) NEXUS FORMAT TREE. This format is used by several popular phylogeny programs,\n"
-"including PAUP and MacClade. The format is described fully in:\n"
-"Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997.\n"
-"NEXUS: an extensible file format for systematic information.\n"
-"Systematic Biology 46:590-621.\n"
-"\n"
-"5) TOGGLE PHYLIP BOOTSTRAP POSITIONS\n"
-"By default, the bootstrap values are placed on the nodes of the phylip format\n"
-"output tree. This is inaccurate as the bootstrap values should be associated\n"
-"with the tree branches and not the nodes. However, this format can be read and\n"
-"displayed by TreeTool, TreeView and Phylowin. An option is available to\n"
-"correctly place the bootstrap values on the branches with which they are\n"
-"associated.\n"
-"";
- sections.push_back(s);
-
-
- // mark
- // replace-string " \"
- // replace-regexp ^ "
- // replace-regexp $ \\n"
-
- // std::cout << "exiting Help::Help" << "\n";
-}
-Help::~Help()
-{
- sections.clear();
-}
-
-
-vector<string> Help::ListSectionMarkers()
-{
- vector<string> markers;
- for (unsigned int i=0; i<this->sections.size(); i++) {
- markers.push_back(this->sections[i].marker);
- }
-
- return markers;
-}
-
-
-string Help::GetSection(char marker)
-{
- string s(1, marker);
- return GetSection(s);
-}
-
-string Help::GetSection(string marker)
-{
- for (unsigned int i=0; i<this->sections.size(); i++) {
- if (this->sections[i].marker == marker) {
- return this->sections[i].content;
- }
- }
- return "";
-}
-
-string Help::GetSectionTitle(char marker)
-{
- string s(1, marker);
- return GetSectionTitle(s);
-}
-string Help::GetSectionTitle(string marker)
-{
- for (unsigned int i=0; i<this->sections.size(); i++) {
- if (this->sections[i].marker == marker) {
- return this->sections[i].title;
- }
- }
- return "";
-}
git://source.jalview.org / jabaws.git / blobdiff